Professor Alan Mark
Affil Professorial Research Fellow
Institute for Molecular Bioscience
Researcher biography
We use computer based modelling techniques to understand and predict the the structural and dynamic properties of (bio)molecules including proteins and lipid aggregates.
Born in 1961, I obtained a BSc (Hon 1) at the University of Sydney in 1982. I obtained my PhD in 1986 from the John Curtin School of Medical Research, Australian National University (ANU), on the "Binding Responses Associated with Self-Interacting Ligands: Studies on the Self-Association and Receptor binding of Insulin". After holding postdoctoral positions at the ANU, University of Groningen, The Netherlands and the Federal Institute of Technology (ETH), Zurich, Switzerland I was appointed Professor of Biophysical Chemistry (Molecular Simulation) University of Groningen, in 1998. In 1998 I also received the Swiss Ruzicka Prize for research in Chemistry for work on simulating peptide folding. In 2004 I was awarded an ARC Federation Fellowship and in February 2005 an honorary chair (Bijzonder Hoogleraar) at the University of Groningen, The Netherlands. I have given over 90 invited lectures at conferences and academic Institutions around the world as well as at a range of summer and winter schools on advanced simulation techniques.
In my research I have performed pioneering simulations of a variety of important biological phenomena, including some of the first atomic simulations of protein unfolding and the first simulations of reversible peptide folding in a realistic environment. In recent years my group performed some of the first atomic and near atomic simulations of the spontaneous aggregation of surfactant and lipid systems into micelles, bilayers and vesicles. These have enabled us, amongst other things, to elucidate the mechanism by which pores are induced within biological membranes in unprecedented detail. Over the last decade I have been intimately involved in the development of the GROMOS force field which is specifically tuned for protein and peptide folding simulations and as well as the development of models for a range of solvents including methanol and trifluoroethanol. I have also been responsible for the development of methodology for the calculations of the thermodynamic properties of biomolecular systems such as free energies of binding and hydration, as well as estimating entropic effects from simulations. Most recently, I have been responsible for the development of novel approaches to promote structure formation in protein folding simulations that can be used for the refinement of protein structures generated by ab initio or by homology methods. Finally, I am associated with two, internationally recognised, (bio)molecular simulation packages the GROningen Molecular Simulation library (GROMOS) and the GROningen Machine for Chemical Simulations (GROMACS).
Book Chapters
Poger, David and Mark, Alan E. (2013). Study of proteins and peptides at interfaces by molecular dynamics simulation techniques. In Juan M Ruso and Angel Pineiro (Ed.), Proteins in solution and at interfaces: methods and applications in biotechnology and materials science (pp. 291-313) Hoboken NJ, United States: John Wiley & Sons, Inc.. doi:10.1002/9781118523063.ch14
Chipot, C., Mark, A. E., Pande, V. S. and Simonson, T. (2007). Applications of Free Energy Calculations to Chemistry and Biology.. In Christophe Chipot and Andrew Pohorille (Ed.), Free Energy Calculations Theory and Applications in Chemistry and Biology (pp. 463-492) Berlin ; New York: Springer.
Journal Articles
Malde, Alpeshkumar K., Stroet, Martin, Caron, Bertrand, Visscher, Koen M. and Mark, Alan E. (2018) Predicting the prevalence of alternative Warfarin tautomers in solution. Journal of Chemical Theory and Computation, . doi:10.1021/acs.jctc.8b00453
Zaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018) Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 3: 630-640. doi:10.1021/acs.jcim.7b00353
Condic-Jurkic, Karmen, Subramanian, Nandhitha, Mark, Alan E. and O'Mara, Megan L. (2018) The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment. PloS One, 13 1: 1-24. doi:10.1371/journal.pone.0191882
Blaskovich, Mark A. T., Hansford, Karl A., Butler, Mark S., Jia, ZhiGuang, Mark, Alan E. and Cooper, Matthew A. (2018) Developments in Glycopeptide Antibiotics. ACS Infectious Diseases, 4 5: 715-735. doi:10.1021/acsinfecdis.7b00258
van Gunsteren, Wilfred F., Daura, Xavier, Hansen, Niels, Mark, Alan E., Oostenbrink, Chris, Riniker, Sereina and Smith, Lorna J. (2017) Validation of Molecular Simulation: An Overview of Issues. Angewandte Chemie - International Edition, 57 4: 884-902. doi:10.1002/anie.201702945
Stroet, Martin, Koziara, Katarzyna B, Malde, Alpeshkumar K and Mark, Alan E (2017) Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach. Journal of chemical theory and computation, 13 12: 6201-6212. doi:10.1021/acs.jctc.7b00800
Lee, Thomas, Caron, Bertrand, Stroet, Martin, Huang, David M., Burn, Paul L. and Mark, Alan E. (2017) The Molecular Origin of Anisotropic Emission in an Organic Light-Emitting Diode. Nano Letters, 17 10: 6464-6468. doi:10.1021/acs.nanolett.7b03528
Schumann-Gillett, Alexandra, Mark, Alan E., Deplazes, Evelyne and O'Mara, Megan L. (2017) A potential new, stable state of the E-cadherin strand-swapped dimer in solution. European Biophysics Journal, . doi:10.1007/s00249-017-1229-3
Reisser, Sabine, Poger, David, Stroet, Martin and Mark, Alan E. (2017) Real cost of speed: the effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulations. Journal of Chemical Theory and Computation, 13 6: 2367-2372. doi:10.1021/acs.jctc.7b00178
Corbett, Michael S. P., Mark, Alan E. and Poger, David (2017) Do all X-ray structures of protein-ligand complexes represent functional states? EPOR, a case study. Biophysical Journal, 112 4: 595-604. doi:10.1016/j.bpj.2016.12.042
Tonnelé, Claire, Stroet, Martin, Caron, Bertrand, Clulow, Andrew J., Nagiri, Ravi C. R., Malde, Alpeshkumar K., Burn, Paul L., Gentle, Ian R., Mark, Alan E. and Powell, Benjamin J. (2017) Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films. Angewandte Chemie - International Edition, 56 29: 8402-8406. doi:10.1002/anie.201610727
Tonnelé, Claire, Stroet, Martin, Caron, Bertrand, Clulow, Andrew J., Nagiri, Ravi C. R., Malde, Alpeshkumar K., Burn, Paul L., Gentle, Ian R., Mark, Alan E. and Powell, Benjamin J. (2017) Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films. Angewandte Chemie, 129 29: 8522-8526. doi:10.1002/ange.201610727
van Gunsteren, Wilfred F., Allison, Jane R., Daura, Xavier, Dolenc, Jožica, Hansen, Niels, Mark, Alan E., Oostenbrink, Chris, Rusu, Victor H. and Smith, Lorna J. (2016) Deriving structural information from experimentally measured data on biomolecules. Angewandte Chemie International Edition, 55 52: 15990-16010. doi:10.1002/anie.201601828
van Gunsteren, Wilfred F., Allison, Jane R., Daura, Xavier, Dolenc, Jožica, Hansen, Niels, Mark, Alan E., Oostenbrink, Chris, Rusu, Victor H. and Smith, Lorna J. (2016) Bestimmung von strukturinformation aus experimentellen messdaten für biomoleküle. Angewandte Chemie, 128 52: 16222-16244. doi:10.1002/ange.201601828
Casey, Lachlan W., Lavrencic, Peter, Bentham, Adam R., Cesari, Stella, Ericsson, Daniel J., Croll, Tristan, Turk, Dušan, Anderson, Peter A., Mark, Alan E., Dodds, Peter N., Mobli, Mehdi, Kobe, Bostjan and Williams, Simon J. (2016) The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins. Proceedings of the National Academy of Sciences, 113 45: 12856-12861. doi:10.1073/pnas.1609922113
Troeira Henriques, Sonia, Deplazes, Evelyne, Lawrence, Nicole, Cheneval, Olivier, Chaousis, Stephanie, Inserra, Marco, Thongyoo, Panumart, King, Glenn F., Mark, Alan E., Vetter, Irina, Craik, David J. and Schroeder, Christina Ingrid (2016) Interaction of tarantula venom peptide ProTx-II with lipid membranes is a prerequisite for its inhibition of human voltage-gated sodium channel NaV1.7. The Journal of Biological Chemistry, 291 33: 17049-17065. doi:10.1074/jbc.M116.729095
Corbett, Michael S. P., Poger, David and Mark, Alan E. (2016) Revisiting the scissor-like mechanism of activation for the erythropoietin receptor. FEBS Letters, 590 18: 3083-3088. doi:10.1002/1873-3468.12340
Adams, Paul D., Aertgeerts, Kathleen, Bauer, Cary, Bell, Jeffrey A., Berman, Helen M., Bhat, Talapady N., Blaney, Jeff M., Bolton, Evan, Bricogne, Gerard, Brown, David, Burley, Stephen K., Case, David A., Clark, Kirk L., Darden, Tom, Emsley, Paul, Feher, Victoria A., Feng, Zukang, Groom, Colin R., Harris, Seth F., Hendle, Jorg, Holder, Thomas, Joachimiak, Andrzej, Kleywegt, Gerard J., Krojer, Tobias, Marcotrigiano, Joseph, Mark, Alan E., Markley, John L., Miller, Matthew, Minor, Wladek, Montelione, Gaetano T., Murshudov, Garib, Nakagawa, Atsushi, Nakamura, Haruki, Nicholls, Anthony, Nicklaus, Marc, Nolte, Robert T., Padyana, Anil K., Peishoff, Catherine E., Pieniazek, Susan, Read, Randy J., Shao, Chenghua, Sheriff, Steven, Smart, Oliver, Soisson, Stephen, Spurlino, John, Stouch, Terry, Svobodova, Radka, Tempel, Wolfram, Terwilliger, Thomas C., Tronrud, Dale, Velankar, Sameer, Ward, Suzanna C., Warren, Gregory L., Westbrook, John D., Williams, Pamela, Yang, Huanwang and Young, Jasmine (2016) Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. Structure, 24 4: 502-508. doi:10.1016/j.str.2016.02.017
Subramanian, Nandhitha, Schumann-Gillett, Alexandra, Mark, Alan E. and O'Mara, Megan L. (2016) Understanding the accumulation of P-glycoprotein substrates within cells: The effect of cholesterol on membrane partitioning. Biochimica et Biophysica Acta: Biomembranes, 1858 4: 776-782. doi:10.1016/j.bbamem.2015.12.025
Poger, David, Caron, Bertrand and Mark, Alan E. (2016) Validating lipid force fields against experimental data: progress, challenges and perspectives.. Biochimica et Biophysica Acta, 1858 7: 1556-1565. doi:10.1016/j.bbamem.2016.01.029
Deplazes, Evelyne, Troeira Henriques, Sonia, Smith, Jennifer J., King, Glenn F., Craik, David J., Mark, Alan E. and Schroeder, Christina I. (2016) Membrane-binding properties of gating modifier and pore-blocking toxins: membrane interaction is not a prerequisite for modification of channel gating. Biochimica et Biophysica Acta - Biomembranes, 1858 4: 872-882. doi:10.1016/j.bbamem.2016.02.002
Deplazes, Evelyne, Davies, Josephine, Bonvin, Alexandre M. J. J., King, Glenn F. and Mark, Alan E. (2016) Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a. Journal of Chemical Information and Modeling, 56 1: 127-138. doi:10.1021/acs.jcim.5b00529
Poger, David and Mark, Alan E. (2015) Effect of Ring Size in ω-Alicyclic Fatty Acids on the Structural and Dynamical Properties Associated with Fluidity in Lipid Bilayers. Langmuir, 31 42: 11574-11582. doi:10.1021/acs.langmuir.5b02635
Saez, Natalie J., Deplazes, Evelyne, Cristofori-Armstrong, Ben, Chassagnon, Irene R., Lin, Xiaozhen, Mobli, Mehdi, Mark, Alan E., Rash, Lachlan D. and King, Glenn F. (2015) Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a. British Journal of Pharmacology, 172 20: 4985-4995. doi:10.1111/bph.13267
Go, Rob Marc, Mark, Alan E., Malde, Alpeshkumar K. and Gilbert, Robert G. (2015) Binding of starch fragments to the starch branching enzyme: implications for developing slower-digesting starch. Biomacromolecules, 16 8: 2475-2481. doi:10.1021/acs.biomac.5b00710
Subramanian, Nandhitha, Condic-Jurkic, Karmen, Mark, Alan E. and O'Mara, Megan L. (2015) Identification of possible binding sites for morphine and nicardipine on the multidrug transporter P-Glycoprotein using umbrella sampling techniques. Journal of Chemical Information and Modeling, 55 6: 1202-1217. doi:10.1021/ci5007382
Poger, David and Mark, Alan E. (2015) A ring to rule them all: the effect of cyclopropane fatty acids on the fluidity of lipid bilayers. Journal of Physical Chemistry B, 119 17: 5487-5495. doi:10.1021/acs.jpcb.5b00958
Li, Cheng, Wu, Alex Chi, Go, Rob Marc, Malouf, Jacob, Turner, Mark S., Malde, Alpeshkumar K., Mark, Alan E. and Gilbert, Robert G. (2015) The characterization of modified starch branching enzymes: toward the vontrol of starch chain-length distributions. PLoS One, 10 4: 1-21. doi:10.1371/journal.pone.0125507
Poger, David, Caron, Bertrand and Mark, Alan E. (2014) Effect of methyl-branched fatty acids on the structure of lipid bilayers. Journal of Physical Chemistry B, 118 48: 13838-13848. doi:10.1021/jp503910r
Caron, Bertrand, Mark, Alan E. and Poger, David (2014) Some like it hot: the effect of sterols and hopanoids on lipid ordering at high temperature. Journal of Physical Chemistry Letters, 5 22: 3953-3957. doi:10.1021/jz5020778
Brooks, Andrew J., Dai, Wei, O’Mara, Megan L., Abankwa, Daniel, Chhabra, Yash, Pelekanos, Rebecca A., Gardon, Olivier, Tunny, Kathryn A., Blucher, Kristopher M., Morton, Craig J., Parker, Michael W., Sierecki, Emma, Gambin, Yann, Gomez, Guillermo A., Alexandrov, Kirill, Wilson, Ian A., Doxastakis, Manolis, Mark, Alan E. and Waters, Michael J. (2014) Mechanism of activation of protein kinase JAK2 by the growth hormone receptor. Science, 344 6185: 1249783.1-1249783.12. doi:10.1126/science.1249783
Poger, David and Mark, Alan E. (2014) Activation of the epidermal growth factor receptor: a series of twists and turns. Biochemistry, 53 16: 2710-2721. doi:10.1021/bi401632z
Jia, ZhiGuang, Ghai, Rajesh, Collins, Brett M. and Mark, Alan E. (2014) The recognition of membrane-bound PtdIns3P by PX domains. Proteins: structure, function, and bioinformatics, 82 10: 2332-2342. doi:10.1002/prot.24593
O'Mara, Megan L. and Mark, Alan E. (2014) Structural characterization of two metastable ATP-bound states of P-glycoprotein. PLoS One, 9 3: e91916.1-e91916.14. doi:10.1371/journal.pone.0091916
Reimers, Jeffrey R., McKemmish, Laura K., McKenzie, Ross H., Mark, Alan E. and Hush, Noel S. (2014) The revised Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not scientifically justified. Comment on "Consciousness in the universe: A review of the 'Orch OR' theory" by Hameroff and Penrose. Physics of Life Reviews, 11 1: 101-103. doi:10.1016/j.plrev.2013.11.003
Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2014) Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. Journal of Computer-Aided Molecular Design, 28 3: 221-233. doi:10.1007/s10822-014-9713-7
Casey, Lachlan W., Mark, Alan E. and Kobe, Bostjan (2014) Small-Angle X-Ray Scattering for the Discerning Macromolecular Crystallographer. Australian Journal of Chemistry, 67 12: 1786-1792. doi:10.1071/CH14396
Xue, Ying, He, Lizhong, Middelberg, Anton P. J., Mark, Alan E. and Poger, David (2014) Determining the structure of interfacial peptide films: comparing neutron reflectometry and molecular dynamics simulations. Langmuir, 30 33: 10080-10089. doi:10.1021/la501715h
Jena, Nihar R., Mark, Alan E. and Mishra, Phool C. (2014) Does tautomerization of FapyG influence its mutagenicity?. ChemPhysChem, 15 9: 1779-1784. doi:10.1002/cphc.201400045
Poger, David and Mark, Alan E. (2013) The relative effect of sterols and hopanoids on lipid bilayers: when comparable is not identical. Journal of Physical Chemistry B, 117 50: 16129-16140. doi:10.1021/jp409748d
Canzar, Stefan, El-Kebir, Mohammed, Pool, René, Elbassioni, Khaled, Malde, Alpeshkumar K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2013) Charge group partitioning in biomolecular simulation. Journal of Computational Biology, 20 3: 188-198. doi:10.1089/cmb.2012.0239
Jia, ZhiGuang, O'Mara, Megan L., Zuegg, Johannes, Cooper, Matthew A. and Mark, Alan E. (2013) Vancomycin: ligand recognition, dimerization and super-complex formation. FEBS Journal, 280 5: 1294-1307. doi:10.1111/febs.12121
Jia, Z. G., O'Mara, M. L., Zuegg, J., Matthew Cooper and Mark, Alan (2013) Erratum: The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II (Biophysical Journal (2011) 101 (2684-2692)). Biophysical Journal, 104 2: 516-516. doi:10.1016/j.bpj.2012.12.031
Poger, David and Mark, Alan E. (2012) Lipid bilayers: the effect of force field on ordering and dynamics. Journal of Chemical Theory and Computation, 8 11: 4807-4817. doi:10.1021/ct300675z
Hughes, Zak E., Mark, Alan E. and Mancera, Ricardo L. (2012) Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranes. Journal of Physical Chemistry B, 116 39: 11911-11923. doi:10.1021/jp3035538
Huenenberger, Philippe H., Mark, Alan E. and Berendsen, Herman J. C. (2012) Wilfred van Gunsteren: 35 years of biomolecular simulation. Journal of Chemical Theory and Computation, 8 10: 3425-3429. doi:10.1021/ct300692s
Fan, Hao, Periole, Xavier and Mark, Alan E. (2012) Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models. Proteins: Structure, Function, and Bioinformatics, 80 7: 1744-1754. doi:10.1002/prot.24068
Seviour, Thomas, Malde, Alpeshkumar K., Kjelleberg, Staffan, Yuan, Zhiguo and Mark, Alan E. (2012) Molecular dynamics unlocks atomic level self-assembly of the exopolysaccharide matrix of water-treatment granular biofilms. Biomacromolecules, 13 6: 1965-1972. doi:10.1021/bm3005808
O’Mara, Megan L. and Mark, Alan E. (2012) The effect of environment on the structure of a membrane protein: P-glycoprotein under physiological conditions. Journal of Chemical Theory and Computation, 8 10: 3964-3976. doi:10.1021/ct300254y
Nair, Pramod C., Malde, Alpeshkumar K., Drinkwater, Nyssa and Mark, Alan E. (2012) Missing fragments: Detecting cooperative binding in fragment-based drug design. ACS Medicinal Chemistry Letters, 3 4: 322-326. doi:10.1021/ml300015u
Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris and Mark, Alan E. (2011) An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7 12: 4026-4037. doi:10.1021/ct200196m
Jia, ZhiGuang, O'Mara, Megan L., Zuegg, Johannes, Cooper, Matthew A. and Mark, Alan E. (2011) The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II. Biophysical Journal, 101 11: 2684-2692. doi:10.1016/j.bpj.2011.10.047
Hoang, Huy N., Driver, Russell W., Beyer, Renée L., Malde, Alpeshkumar K., Le, Giang T., Abbenante, Giovanni, Mark, Alan E. and Fairlie, David P. (2011) Protein a-turns recreated in structurally stable small molecules. Angewandte Chemie International Edition, 123 47: 11303-11307. doi:10.1002/ange.201105119
Saez, Natalie J., Mobli, Mehdi, Bieri, Michael, Chassagnon, Irene R., Malde, Alpeshkumar K., Gamsjaeger, Roland, Mark, Alan E., Gooley, Paul R., Rash. Lachlan D. and King, Glenn F. (2011) A dynamic pharmacophore drives the interaction between psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a. Molecular Pharmacology, 80 5: 796-808. doi:10.1124/mol.111.072207
Riniker, Sereina, Christ, Clara D., Hansen, Niels, Mark, Alan E., Nair, Pramod C. and van Gunsteren, Wilfred F. (2011) Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. Journal of Chemical Physics, 135 2: 024105.1-024105.13. doi:10.1063/1.3604534
Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E. and van Gunsteren, Wilfred F. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. European Biophysics Journal, 40 7: 843-856. doi:10.1007/s00249-011-0700-9
Nair, Pramod C., Malde, Alpeshkumar K. and Mark, Alan E. (2011) Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT). Journal of Chemical Theory and Computation, 7 5: 1458-1468. doi:10.1021/ct1007229
Chen, Rong and Mark, Alan E. (2011) The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of action. European Biophysics Journal, 40 4: 545-553. doi:10.1007/s00249-011-0677-4
Chen, Rong, Poger, David and Mark, Alan (2011) Effect of high pressure on fully hydrated DPPC and POPC bilayers. The Journal of Physical Chemistry B, 115 5: 1038-1044. doi:10.1021/jp110002q
Xue, Ying, O'Mara, Megan L., Surawski, Peter P. T., Trau, Matt and Mark, Alan E. (2011) Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: A molecular dynamics study. Langmuir, 27 1: 296-303. doi:10.1021/la103800h
Malde, AK and Mark, AE (2011) Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. Journal of Computer-Aided Molecular Design, 25 1: 1-12. doi:10.1007/s10822-010-9397-6
Daura, Xavier, Affentranger, Roman and Mark, Alan E. (2010) On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences. ChemPhysChem, 11 17: 3734-3743. doi:10.1002/cphc.201000562
Groothuizen, Flora S., Poger, David and Mark, Alan E. (2010) Activating the prolactin receptor: Effect of the ligand on the conformation of the extracellular domain. Journal of Chemical Theory and Computation, 6 10: 3274-3283. doi:10.1021/ct1003934
Christ, Clara D., Mark, Alan E. and van Gunsteren, Wilfred F. (2010) Basic ingredients of free energy calculations: A review. Journal of Computational Chemistry, 31 8: 1569-1582. doi:10.1002/jcc.21450
Poger, David, van Gunsteren, Wilfred F. and Mark, Alan E. (2010) A new force field for simulating phosphatidylcholine bilayers. Journal of Computational Chemistry, 31 6: 1117-1125. doi:10.1002/jcc.21396
Poger, David and Mark, Alan E. (2010) Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation. Proteins: Structure, Function & Bioinformatics, 78 5: 1163-1174. doi:10.1002/prot.22636
Poger, David and Mark, Alan E. (2010) On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experiment. Journal of Chemical Theory and Computation, 6 1: 325-336. doi:10.1021/ct900487a
McKemmish, Laura K., Reimers, Jeffrey R., McKenzie, Ross H., Mark, Alan E. and Hush, Noel S. (2009) Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible. Physical Review E, 80 2: 1-5. doi:10.1103/PhysRevE.80.021912
Periole, Xavier, Rampioni, Aldo, Vendruscolo, Michele and Mark, Alan E. (2009) Factors That Affect the Degree of Twist in beta-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-beta Filament of the GNNQQNY Peptide (vol 113, pg 1728, 2009). Journal of Physical Chemistry B, 113 30: 10548-10548. doi:10.1021/jp905822d
Yesylevskyy, Semen, Marrink, Siewert-Jan and Mark, Alan E. (2009) Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers. Biophysical Journal, 97 1: 40-49. doi:10.1016/j.bpj.2009.03.059
Donnini, Serena, Villa, Alessandra, Groenhof, Gerrit, Mark, Alan E., Wierenga, Rik K. and Juffer, Andre H. (2009) Inclusion of ionization states of ligands in affinity calculations. Proteins: Structure, Function and Bioinformatics, 76 1: 138-150. doi:10.1002/prot.22326
Periole, Xavier, Allen, Lucy R., Tamiola, Kamil, Mark, Alan E. and Paci, Emanuele (2009) Probing the free energy landscape of the FBP28WW domain using multiple techniques. Journal of Computational Chemistry, 30 7: 1059-1068. doi:10.1002/jcc.21128
Siwko, Magdalena E., de Vries, Alex H., Mark, Alan E., Kozubek, Arkadiusz and Marrink, Siewert J. (2009) Disturb or stabilize? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers. Biophysical Journal, 96 8: 3140-3153. doi:10.1016/j.bpj.2009.01.040
Reimers, Jeffrey R., McKemmish, Laura K., McKenzie, Ross H., Mark, Alan E. and Hush, Noel S. (2009) Weak, strong, and coherent regimes of Frohlich condensation and their applications to terahertz medicine and quantum consciousness. Proceedings of the National Academy of Sciences of USA, 106 11: 4219-4224. doi:10.1073/pnas.0806273106
Malde, Alpeshkumar K. and Mark, Alan E. (2009) Binding and enantiomeric selectivity of threonyl-tRNA synthetase. Journal of the American Chemical Society, 131 11: 3848-3849. doi:10.1021/ja9002124
Periole, Xavier, Rampioni, Aldo, Vendruscolo, Michele and Mark, Alan E. (2009) Factors that affect the degree of twist in beta-sheet structures: A molecular dynamics simulation study of a cross-beta filament of the GNNQQNY peptide. The Journal of Physical Chemistry Part B, 113 6: 1728-1737. doi:10.1021/jp8078259
Wassenaar, Tsjerk A., Daura, Xavier, Padros, Esteve and Mark, Alan E. (2009) Calcium binding to the purple membrane: A molecular dynamics study. Proteins Structure Function Bioinformatics, 74 3: 669-681. doi:10.1002/prot.22182
Sengupta, Durba, Leontidaou, Hari, Mark, Alan E. and Marrink, Siewert-Jan (2008) Toroidal pores formed by antimicrobial peptides show significant disorder. Biochimica et Biophysica Acta: Biomembranes, 2008 1778: 2308-2317. doi:10.1016/j.bbamem.2008.06.007
Kwan, Ann H., Macindoe, Ingrid, Vukasin, Paul V., Morris, Vanessa K., Kass, Itamar, Gupte, Rima, Mark, Alan E., Templeton, Matthew D., Mackay, Joel P. and Sunde, Margaret (2008) The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. Journal of Molecular Biology, 382 3: 708-720. doi:10.1016/j.jmb.2008.07.034
Risselada, H. Jelger, Mark, Alan E. and Marrink, Siewert J. (2008) Application of mean field boundary potentials in simulations of lipid vesicles. The Journal of Physical Chemistry B, 112 25: 7438-7447. doi:10.1021/jp0758519
Cemazar, M., Joshi, A., Daly, N. L., Mark, A. E. and Craik, D. J. (2008) The structure of a two-disulfide intermediate assists in elucidating the oxidative folding pathway of a cyclic cystine knot protein. Structure, 16 6: 842-851. doi:10.1016/j.str.2008.02.023
Zhu, J., Fan, H., Periole, X., Honig, B. and Mark, A.E. (2008) Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins Structure Function Bioinformatics, 72 72: 1171-1188. doi:10.1002/prot.22005
Knecht, V., Risselda, H. J., Mark, A. E. and Marrink, S. J. (2008) Electrophoretic mobility does not always reflect the charge on an oil droplet. Journal of Colloid and Interface Science, 318 2: 477-486. doi:10.1016/j.jcis.2007.10.035
van Gunsteren, W.F., Dolenc, J. and Mark, A.E. (2008) Molecular simulation as an aid to experimentalists. Current Opinion In Structural Biology, 2008 18: 149-153. doi:10.1016/j.sbi.2007.12.007
Wassenaar, Tsjerk A., Quax, Wim J. and Mark, Alan E. (2008) The conformation of the extracellular binding domain of Death Receptor 5 in the presence and absence of the activating ligand TRAIL: A molecular dynamics study. Proteins: Structure, Function, and Bioinformatics, 70 2: 333-343. doi:10.1002/prot.21541
Mueller, D., Kampmann, T., Yennamalli, R., Young, P.R., Kobe, B. and Mark, A. E. (2008) Histidine protonation and the activation of viral fusion proteins. Biochemical Society Transactions, 36 1: 43-45. doi:10.1042/BST0360043
Chipot, Christophe, Mark, Alan E., Pande, Vijay S. and Simonson, Thomas (2007) Applications of free energy calculations to chemistry and biology. Springer Series in Chemical Physics, 86 463-501. doi:10.1007/978-3-540-38448-9_13
Leontiadou, H, Mark, AE and Marrink, SJ (2007) Ion transport across transmembrane pores. Biophysical Journal, 92 12: 4209-4215. doi:10.1529/biophysj.106.101295
Villa, A, Fan, H, Wassenaar, T and Mark, AE (2007) How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?. Journal of Physical Chemistry B, 111 21: 6015-6025. doi:10.1021/jp068580v
Pineiro, Ángel, Banquy, Xavier, Perez-Casas, Silvia, Tovar, Edgar, Garcia, Abel, Villa, Alessandra, Amigo, Alfredo, Mark, Alan E. and Costas, Miguel (2007) On the characterization of host-guest complexes: Surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant. Journal of Physical Chemistry B, 111 17: 4383-4392. doi:10.1021/jp0688815
Periole, X, Vendruscolo, M and Mark, AE (2007) Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain. Proteins-structure Function And Bioinformatics, 69 3: 536-550. doi:10.1002/prot.21491
Periole, X and Mark, AE (2007) Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. Journal of Chemical Physics, 126 1: 014903-1-014903-11. doi:10.1063/1.2404954
Siwko, M. E., Marrink, S. J., de Vries, A. H., Kozubek, A., Uiterkamp, A. J. M. S. and Mark, A. E. (2007) Does isoprene protect plant membranes from thermal shock? A molecular dynamics study. Biochimica Et Biophysica Acta-biomembranes, 1768 2: 198-206. doi:10.1016/j.bbamem.2006.09.023
Fan, Hao and Mark, Alan E. (2006) Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures. Protein Science, 15 3: 441-448. doi:10.1110/ps.051721006
Knecht, V., Mark, A. E. and Marrink, S. J. (2006) Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail. Journal of The American Chemical Society, 128 6: 2030-2034. doi:10.1021/ja056619a
Wassenaar, T. A. and Mark, A. E. (2006) The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. Journal of Computational Chemistry, 27 3: 316-325. doi:10.1002/jcc.20341
Villa, A., Mark, A. E., Saracino, G. A. A., Cosentino, U., Pitea, D., Moro, G and Salmona, M. (2006) Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics study. Journal of Physical Chemistry B, 110 3: 1423-1428. doi:10.1021/jp052722o
Kampmann, Thorsten, Meuller, Daniela S., Mark, Alan E., Young, Paul R. and Kobe, Bostjan (2006) The role of histidine residues in low-pH-mediated viral membrane fusion. Structure, 14 10: 1481-1487. doi:10.1016/j.str.2006.07.011
Fan, Hao, Wang, Xiaoqin, Zhu, Jiang, Robillard, George T. and Mark, Alan E. (2006) Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface. Proteins-structure Function And Bioinformatics, 64 4: 863-873. doi:10.1002/prot.20936
Leontiadou, H., Mark, A. E. and Marrink, S. J. (2006) Antimicrobial peptides in action. Journal of The American Chemical Society, 128 37: 12156-12161. doi:10.1021/ja062927q
Pineiro, A., Villa, A., Vagt, T., Koksch, B. and Mark, A. E. (2005) A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations. Biophysical Journal, 89 6: 3701-3713. doi:10.1529/biophysj.104.055590
van den Bosch, M., Swart, M., Snijders, J. G., Berendsen, H. J. C., Mark, A. E., Oostenbrink, C., van Gunsteren, W. F. and Canters, G. W. (2005) Calculation of the redox potential of the protein azurin and some mutants. Chembiochem, 6 4: 738-746. doi:10.1002/cbic.200400244
Knecht, V., Muller, M., Bonn, M., Marrink, S. J. and Mark, A. E. (2005) Simulation studies of pore and domain formation in a phospholipid monolayer. Journal of Chemical Physics, 122 2: 024704.1-024704.9. doi:10.1063/1.1825992
Pagel, K., Seeger, K., Seiwert, B., Villa, A., Mark, A. E., Berger, S. and Koksch, B. (2005) Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide. Organic & Biomolecular Chemistry, 3 7: 1189-1194. doi:10.1039/b418167k
Kovalskyy, D., Dubyna, V., Mark, A. E. and Kornelyuk, A. (2005) A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site. Proteins-structure Function And Bioinformatics, 58 2: 450-458. doi:10.1002/prot.20304
Soto, P., Cladera, J., Mark, A. E. and Daura, X. (2005) Stability of SIV gp32 fusion-peptide single-layer protofibrils as monitored by molecular-dynamics simulations. Angewandte Chemie-international Edition, 44 7: 1065-1067. doi:10.1002/anie.200461935
Donnini, S., Mark, A. E., Juffer, A. H. and Villa, A. (2005) Incorporating the effect of ionic strength in free energy calculations using explicit ions. Journal of Computational Chemistry, 26 2: 115-122. doi:10.1002/jcc.20156
Fan, Hao, Mark, Alan E., Zhu, Jiang and Honig, Barry (2005) Comparative study of generalized Born models: Protein dynamics. Proceedings of The National Academy of Sciences of The United States of America, 102 19: 6760-6764. doi:10.1073/pnas.0408857102
de Vries, Alex H., Yefimov, Serge, Mark, Alan E. and Marrink, Siewert J. (2005) Molecular structure of the lecithin ripple phase. Proceedings of The National Academy of Sciences of The United States of America, 102 15: 5392-5396. doi:10.1073/pnas.0408249102
Marrink, S. J., Risselada, J. and Mark, A. E. (2005) Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model. Chemistry And Physics of Lipids, 135 2: 223-244. doi:10.1016/j.chemphyslip.2005.03.001
Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E. and Berendsen, H. J. C. (2005) GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26 16: 1701-1718. doi:10.1002/jcc.20291
Marrink, S. J. and Mark, A. E. (2004) Molecular View of Hexagonal Phase Formation in Phospholipid Membranes. Biophysical Journal, 87 6: 3894-3900. doi:10.1529/biophysj.104.048710
Oostenbrink, C., Villa, A., Mark, A. E. and Van Gunsteren, W. F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25 13: 1656-1676. doi:10.1002/jcc.20090
Leontiadou, H., Mark, A. E. and Marrink, S. J. (2004) Molecular dynamics simulations of hydrophilic pores in lipid bilayers. Biophysical Journal, 86 4: 2156-2164. doi:10.1016/S0006-3495(04)74275-7
Zangi, R. and Mark, A. E. (2004) Electrofreezing of confined water. Journal of Chemical Physics, 120 15: 7123-7130. doi:10.1063/1.1687315
Fan, H. and Mark, A. E. (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Science, 13 1: 211-220. doi:10.1110/ps.03381404
de Vries, A. H., Mark, A. E. and Marrink, S. J. (2004) The binary mixing behavior of phospholipids in a bilayer: A molecular dynamics study. Journal of Physical Chemistry B, 108 7: 2454-2463. doi:10.1021/jp0366926
de Vries, A. H., Mark, A. E. and Marrink, S. J. (2004) Molecular dynamics simulation of the spontaneous formation of a small DPPC vesicle in water in atomistic detail. Journal of The American Chemical Society, 126 14: 4488-4489. doi:10.1021/ja0398417
Groenhof, G., Bouxin-Cademartory, M., Hess, B., De Visser, S. P., Berendsen, H. J. C., Olivucci, M., Mark, A. E. and Robb, M. A. (2004) Photoactivation of the photoactive yellow protein: Why photon absorption triggers a trans-to-cis lsomerization of the chromophore in the protein. Journal of The American Chemical Society, 126 13: 4228-4233. doi:10.1021/ja039557f
Fan, H. and Mark, A. E. (2004) Mimicking the action of folding chaperones in molecular dynamics simulations: Application to the refinement of homology-based protein structures. Protein Science, 13 4: 992-999. doi:10.1110/ps.03449904
Marrink, S. J., de Vries, A. H. and Mark, A. E. (2004) Coarse grained model for semiquantitative lipid simulations. Journal of Physical Chemistry B, 108 2: 750-760. doi:10.1021/jp036508g
Zangi, R. and Mark, A. E. (2003) Monolayer ice. Physical Review Letters, 91 2: 025502-1-025502-4. doi:10.1103/PhysRevLett.91.025502
Colombo, G., Marrink, S. J. and Mark, A. E. (2003) Simulation of MscL Gating in a Bilayer under Stress. Biophysical Journal, 84 4: 2331-2337. doi:10.1016/S0006-3495(03)75038-3
Fan, H. and Mark, A. E. (2003) Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study. Proteins-structure Function And Genetics, 53 1: 111-120. doi:10.1002/prot.10496
Marrink, S. J. and Mark, A. E. (2003) The mechanism of vesicle fusion as revealed by molecular dynamics simulations. Journal of The American Chemical Society, 125 37: 11144-11145. doi:10.1021/ja036138+
Villa, A., Zangi, R., Pieffet, G. and Mark, A. E. (2003) Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. Journal of Computer-aided Molecular Design, 17 10: 673-686. doi:10.1023/B:JCAM.0000017374.53591.32
Fioroni, M., Burger, K., Mark, A. E. and Roccatano, D. (2003) The influence of trifluoromethyl groups on the miscibility of fluorinated alcohols with water: A molecular dynamics simulation study of 1,1,1-trifluoropropan-2-ol in aqueous solution. Journal of Physical Chemistry B, 107 20: 4855-4861. doi:10.1021/jp026076u
Marrink, Siewert J. and Mark, Alan E. (2003) Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. Journal of The American Chemical Society, 125 49: 15233-15242. doi:10.1021/ja0352092
Zangi, R. and Mark, A. E. (2003) Bilayer ice and alternate liquid phases of confined water. Journal of Chemical Physics, 119 3: 1694-1700. doi:10.1063/1.1580101
Talhout, R., Villa, A., Mark, A. E. and Engberts, J. B. F. N. (2003) Understanding binding affinity: A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin. Journal of The American Chemical Society, 125 35: 10570-10579. doi:10.1021/ja034676g
Tieleman, D. P., Leontiadou, H., Mark, A. E. and Marrink, S. J. (2003) Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. Journal of The American Chemical Society, 125 21: 6382-6383. doi:10.1021/ja029504i
Zangi, R., de Vocht, M. L., Robillard, G. T. and Mark, A. E. (2002) Molecular Dynamics Study of the Folding of Hydrophobin SC3 at a Hydrophilic/Hydrophobic Interface. Biophysical Journal, 83 1: 112-124. doi:10.1016/S0006-3495(02)75153-9
Groenhof, G., Lensink, M. F., Berendsen, H. J. C. and Mark, A. E. (2002) Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes. Proteins-structure Function And Genetics, 48 2: 212-219. doi:10.1002/prot.10135
Feenstra, K. A., Peter, C., Scheek, R. M., van Gunsteren, W. F. and Mark, A. E. (2002) A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. Journal of Biomolecular Nmr, 23 3: 181-194. doi:10.1023/A:1019854626147
Groenhof, G., Lensink, M. F., Berendsen, H. J. C., Snijders, J. G. and Mark, A. E. (2002) Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore. Proteins-structure Function And Genetics, 48 2: 202-211. doi:10.1002/prot.10136
Colombo, G., Roccatano, D. and Mark, A. E. (2002) Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins-structure Function And Genetics, 46 4: 380-392. doi:10.1002/prot.1175
Villa, A. and Mark, A. E. (2002) Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Journal of Computational Chemistry, 23 5: 548-553. doi:10.1002/jcc.10052
Soto, P. and Mark, A. E. (2002) The effect of the neglect of electronic polarization in peptide folding simulations. Journal of Physical Chemistry B, 106 49: 12830-12833. doi:10.1021/jp026526i
Schafer, H., Smith, L. J., Mark, A. E. and van Gunsteren, W. F. (2002) Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactalbumin. Proteins-structure Function And Genetics, 46 2: 215-224. doi:10.1002/prot.1166
Roccatano, D., Colombo, G., Fioroni, M. and Mark, A. E. (2002) Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study. Proceedings of The National Academy of Sciences of The United States of America, 99 19: 12179-12184. doi:10.1073/pnas.182199699
Marrink, S. J. and Mark, A. E. (2002) Molecular dynamics simulations of mixed micelles modeling human bile. Biochemistry, 41 17: 5375-5382. doi:10.1021/bi015613i
van Gunsteren, W. F., Daura, X. and Mark, A. E. (2002) Computation of free energy. Helvetica Chimica Acta, 85 10: 3113-3129.
van den Berg, P. A. W., Feenstra, K. A., Mark, A. E., Berendsen, H. J. C. and Visser, A. J. W. G. (2002) Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics. Journal of Physical Chemistry B, 106 34: 8858-8869. doi:10.1021/jp020356s
Burgi, R., Daura, X., Mark, A. E., Bellanda, M., Mammi, S., Peggion, E. and van Gunsteren, W. (2001) Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. Journal of Peptide Research, 57 2: 107-118. doi:10.1034/j.1399-3011.2001.00793.x
de Groot, B. L., Daura, X., Mark, A. E. and Grubmuller, H. (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology, 309 1: 299-313. doi:10.1006/jmbi.2001.4655
Walser, R., Hess, B., Mark, A. E. and van Gunsteren, W. F. (2001) Further investigation on the validity of Stokes-Einstein behaviour at the molecular level. Chemical Physics Letters, 334 4-6: 337-342. doi:10.1016/S0009-2614(00)01290-2
Roccatano, D., Mark, A. E. and Hayward, S. (2001) Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. Journal of Molecular Biology, 310 5: 1039-1053. doi:10.1006/jmbi.2001.4808
Zangi, R., Kovacs, H., van Gunsteren, W. F., Johansson, J. and Mark, A. E. (2001) Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C. Proteins-structure Function And Genetics, 43 4: 395-402. doi:10.1002/prot.1052
Fioroni, M., Burger, K., Mark, A. E. and Roccatano, D. (2001) Model of 1,1,1,3,3,3-hexafluoro-propan-2-ol for molecular dynamics simulations. Journal of Physical Chemistry B, 105 44: 10967-10975. doi:10.1021/jp012476q
Marrink, S. J., Lindahl, E., Edholm, O. and Mark, A. E. (2001) Simulation of the spontaneous aggregation of phospholipids into bilayers. Journal of The American Chemical Society, 123 35: 8638-8639. doi:10.1021/ja0159618
Marrink, S. J. and Mark, A. E. (2001) Effect of undulations on surface tension in simulated bilayers. Journal of Physical Chemistry B, 105 26: 6122-6127. doi:10.1021/jp0103474
Schafer, H., Daura, X., Mark, A. E. and van Gunsteren, W. F. (2001) Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior. Proteins-structure Function And Genetics, 43 1: 45-56. doi:10.1002/1097-0134(20010401)43:1<45::AID-PROT1016>3.0.CO;2-N
Fioroni, Marco, Burger, Klaus, Mark, Alan E. and Roccatano, Danilo (2000) A new 2,2,2-triflouroethanol model for molecular dynamics simulations. The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces and Biophysical, 104 51: 12347-12354. doi:10.1021/jp002115v
Marrink, S. J., Tieleman, D. P. and Mark, A. E. (2000) Molecular dynamics simulation of the kinetics of spontaneous micelle formation. Journal of Physical Chemistry B, 104 51: 12165-12173. doi:10.1021/jp001898h
Schafer, Heiko, Mark, Alan E. and van Gunsteren, Wilfred F. (2000) Absolute entropies from molecular dynamics simulation trajectories. Journal of Chemical Physics, 113 18: 7809-7817. doi:10.1063/1.1309534
Walser, Regula, Mark, Alan E., van Gunsteren, Wilfred F., Lauterbach, Monika and Wipff, Georges (2000) The effect of force-field parameters on properties of liquids: Parameterization of a simple three site model for methanol. Journal of Chemical Physics, 112 23: 10450-10459. doi:10.1063/1.481680
Walser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (2000) On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperence protein unfolding simulations. Biophysical Journal, 78 6: 2752-2760. doi:10.1016/S0006-3495(00)76820-2
Bonvin, Alexandre M. J. J., Mark, Alan E. and van Gunsteren, Wilfred F. (2000) The GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128 3: 550-557. doi:10.1016/S0010-4655(99)00540-8
Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999) Peptide folding simulations: No solvent required?. Computer Physics Communications, 123 1-3: 97-102. doi:10.1016/S0010-4655(99)00261-1
Schäfer, Heiko, Van Gunsteren, Wilfred F. and Mark, Alan E. (1999) Estimating relative free energies from a single ensemble: Hydration free energies. Journal of Computational Chemistry, 20 15: 1604-1617. doi:10.1002/(SICI)1096-987X(19991130)20:15<1604::AID-JCC2>3.0.CO;2-A
Daura, Xavier, Antes, Iris, van Gunsteren, Wilfred F, Thiel, Walter and Mark, Alan E. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Structure, Function, and Bioinformatics, 36 4: 542-555. doi:10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
Scott, Walter R. P., Hunenberger, Philippe H., Tironi, Ilario G., Mark, Alan E., Billeter, Salomon R., Fennen, Jens, Torda, Andrew E., Huber, Thomas, Kruger, Peter and van Gunsteren, Wilfred F. (1999) The GROMOS biomolecular simulation program package. Journal of Physical Chemistry A, 103 19: 3596-3607. doi:10.1021/jp984217f
Walser, Regula, Mark, Alan E. and van Gunsteren, Wilfred F. (1999) On the validity of Stokes’ law at the molecular level. Chemical Physics Letters, 303 5-6: 583-586. doi:10.1016/S0009-2614(99)00266-3
Daura, X., van Gunsteren, W. F. and Mark, A. E. (1999) Folding-unfolding thermodynamics of a beta-heptapeptide form equilibrium simulations. Proteins: Structure, Function, and Genetics, 34 3: 269-280. doi:10.1002/(SICI)1097-0134(19990215)34:3
Daura, Xavier, Gadermann, Karl, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1999) Peptide Folding: When simulation meets experiment. Angewandte Chemie, 38 1-2: 236-240. doi:10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M
Scott, Walter R. P., Mark, Alan E. and van Gunsteren, W.F. (1998) On using time-averaging restraints in molecular dynamics simulation. Journal of Biomolecular NMR, 12 4: 501-508. doi:10.1023/A:1008306732538
Daura, Xavier, Jaun, Bernhard, Seebach, Dieter, van Gunsteren, Wilfred F. and Mark, Alan E. (1998) Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology, 280 5: 925-932. doi:10.1006/jmbi.1998.1885
Smith, Lorna J., Mark, Alan E., Dobson, Christopher M. and van Gunsteren, Wilfred (1998) Molecular dynamics simulations of peptide fragments from hen lysozyme: Insight into non-native protein conformations. Journal of Molecular Biology, 280 4: 703-719. doi:10.1006/jmbi.1998.1892
Daura, Xavier, Mark, Alan E. and van Gunsteren, Wilfred F. (1998) Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry, 19 5: 535-547. doi:10.1002/(SICI)1096-987X(19980415)19:5<535::AID-JCC6>3.0.CO;2-N
van Gunsteren, Wilfred F. and Mark, Alan E. (1998) Validation of molecular dynamics simulation. Journal of Chemical Physics, 108 15: 6109-6116. doi:10.1063/1.476021
Lauterbach, M, Wipff, G, Mark, A and van Gunsteren, WF (1997) Liquid-liquid ion extraction: Influence of the water content of the organic phase on the ion extraction selectivity. An MD and FEP study of calix[4]crown-6 alkali cation complexes in binary chloroform-water mixtures. Gazzetta Chimica Italiana, 127 11: 699-708.
Kovacs, H, Mark, AE and vanGunsteren, WF (1997) Solvent structure at a hydrophobic protein surface. Proteins-Structure Function and Genetics, 27 3: 395-404. doi:10.1002/(SICI)1097-0134(199703)27:3<395::AID-PROT7>3.0.CO;2-C
Daura, X, Hunenberger, PH, Mark, AE, Querol, E, Aviles, FX and vanGunsteren, WF (1996) Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions. Journal of the American Chemical Society, 118 26: 6285-6294. doi:10.1021/ja9537944
Liu, HY, Mark, AE and vanGunsteren, WF (1996) Estimating the relative free energy of different molecular states with respect to a single reference state. Journal of Physical Chemistry, 100 22: 9485-9494. doi:10.1021/jp9605212
Vangunsteren, WF, Hunenberger, PH, Mark, AE, Smith, PE and Tironi, IG (1995) Computer simulation of protein motion. Computer Physics Communications, 91 1-3: 305-319. doi:10.1016/0010-4655(95)00055-K
Smith, LJ, Mark, AE, Dobson, CM and Vangunsteren, WF (1995) Comparison of Md Simulations and Nmr Experiments for Hen Lysozyme - Analysis of Local Fluctuations, Cooperative Motions, and Global Changes. Biochemistry, 34 34: 10918-10931. doi:10.1021/bi00034a026
Kovacs, H, Mark, AE, Johansson, J and Vangunsteren, WF (1995) The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. Journal of Molecular Biology, 247 4: 808-822. doi:10.1016/S0022-2836(05)80156-1
Vangunsteren, WF, Hunenberger, PH, Kovacs, H, Mark, AE and Schiffer, CA (1995) Investigation of Protein Unfolding and Stability by Computer-Simulation. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 348 1323: 49-59.
Mark, AE, Xu, YW, Liu, HY and vanGunsteren, WF (1995) Rapid non-empirical approaches for estimating relative binding free energies. Acta Biochimica Polonica, 42 4: 525-535.
Hunenberger, PH, Mark, AE and Vangunsteren, WF (1995) Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study. Proteins: Structure, Function and Genetics, 21 3: 196-213. doi:10.1002/prot.340210303
Hunenberger, PH, Mark, AE and Vangunsteren, WF (1995) Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations. Journal of Molecular Biology, 252 4: 492-503. doi:10.1006/jmbi.1995.0514
Vangunsteren, WF, King, PM and Mark, AE (1994) Fundamentals of Drug Design From a Biophysical Viewpoint. Quarterly Reviews of Biophysics, 27 4: 435-481.
Mark, AE, Vanhelden, SP, Smith, PE, Janssen, Lhm and Vangunsteren, WF (1994) Convergence Properties of Free-Energy Calculations - Alpha-Cyclodextrin Complexes as a Case-Study. Journal of the American Chemical Society, 116 14: 6293-6302. doi:10.1021/ja00093a032
Mark, AE and Vangunsteren, WF (1994) Decomposition of the Free-Energy of a System in Terms of Specific Interactions - Implications for Theoretical and Experimental Studies. Journal of Molecular Biology, 240 2: 167-176. doi:10.1006/jmbi.1994.1430
Beutler, TC, Mark, AE, Vanschaik, RC, Gerber, PR and Vangunsteren, WF (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chemical Physics Letters, 222 6: 529-539. doi:10.1016/0009-2614(94)00397-1
Delacruz, X, Mark, AE, Tormo, J, Fita, I and Vangunsteren, WF (1994) Investigation of shape variations in the antibody binding site by molecular dynamics computer simulation. Journal of Molecular Biology, 236 4: 1186-1195. doi:10.1016/0022-2836(94)90020-5
Yunyu, S, Mark, AE, Wang, CX, Huang, FH, Berendsen, Hjc and Vangunsteren, WF (1993) Can the Stability of Protein Mutants Be Predicted by Free-Energy Calculations. Protein Engineering, 6 3: 289-295. doi:10.1093/protein/6.3.289
Smith, PE, Brunne, RM, Mark, AE and Vangunsteren, WF (1993) Dielectric-Properties of Trypsin-Inhibitor and Lysozyme Calculated From Molecular-Dynamics Simulations. Journal of Physical Chemistry, 97 9: 2009-2014. doi:10.1021/j100111a046
Eltayar, N, Mark, AE, Vallat, P, Brunne, RM, Testa, B and Vangunsteren, WF (1993) Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: Evidence from partition coefficients and molecular dynamics simulations. Journal of Medicinal Chemistry, 36 24: 3757-3764. doi:10.1021/jm00076a002
Gerber, PR, Mark, AE and Vangunsteren, WF (1993) An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. Journal of Computer-Aided Molecular Design, 7 3: 305-323. doi:10.1007/BF00125505
Vangunsteren, WF and Mark, AE (1992) Prediction of the activity and stability effects of site-directed mutagenesis on a protein core. Journal of Molecular Biology, 227 2: 389-395. doi:10.1016/0022-2836(92)90895-Q
Mark, AE and Vangunsteren, WF (1992) Simulation of the Thermal-Denaturation of Hen Egg-White Lysozyme - Trapping the Molten Globule State. Biochemistry, 31 34: 7745-7748. doi:10.1021/bi00149a001
Vorherr, T, Kessler, O, Mark, A and Carafoli, E (1992) Construction and Molecular-Dynamics Simulation of Calmodulin in the Extended and in a Bent Conformation. European Journal of Biochemistry, 204 2: 931-937. doi:10.1111/j.1432-1033.1992.tb16714.x
Vangunsteren, WF and Mark, AE (1992) On the Interpretation of Biochemical Data by Molecular-Dynamics Computer-Simulation. European Journal of Biochemistry, 204 3: 947-961.
Mark, AE, Berendsen, Hjc and Vangunsteren, WF (1991) Conformational Flexibility of Aqueous Monomeric and Dimeric Insulin - a Molecular-Dynamics Study. Biochemistry, 30 45: 10866-10872. doi:10.1021/bi00109a009
Mark, AE, Vangunsteren, WF and Berendsen, Hjc (1991) Calculation of Relative Free-Energy Via Indirect Pathways. Journal of Chemical Physics, 94 5: 3808-3816. doi:10.1063/1.459753
Mark, AE and Jeffrey, PD (1990) The self-association of zinc-free bovine insulin four model patterns and their significance. Biological Chemistry Hoppe-Seyler, 371 2: 1165-1174. doi:10.1515/bchm3.1990.371.2.1165
Mark, AE, Nichol, LW and Jeffrey, PD (1990) The Reversible Cross-Linking of Receptors by Ligands - Theory for the Prediction of Binding Responses. Biochemistry International, 22 4: 685-697.
Mark, AE, Jeffrey, PD and Nichol, LW (1988) The binding of an indefinitely associating ligand to acceptor: Consideration of monovalent ligand species binding to a multivalent acceptor. Journal of Theoretical Biology, 131 2: 137-149. doi:10.1016/S0022-5193(88)80231-5
Mark, AE, Nichol, LW and Jeffrey, PD (1987) The self-association of zinc-free bovine insulin. A single model based on interactions in the crystal that describes the association pattern in solution at pH 2, 7 and 10. Biophysical Chemistry, 27 2: 103-117. doi:10.1016/0301-4622(87)80051-0
Stone, SR, Mark, A and Morrison, JF (1984) Interaction of Analogs of Nicotinamide Adenine-Dinucleotide Phosphate with Dihydrofolate-Reductase From Escherichia-Coli. Biochemistry, 23 19: 4340-4346. doi:10.1021/bi00314a014
Conference Papers
Brooks, Andrew, Dai, W., O'Mara, M. L., Abankwa, D., Chhabra, Y., Pelekanos, R. A., Gardon, O., Tunny, K. A., Blucher, K. M., Morton, C. J., Parker, M. W., Sierecki, E., Gambin, Y., Gomez, G. A., Alexandrov, K., Wilson, I. A., Doxastakis, M., Mark, A. E. and Waters, M. J. (2016). Going downstream - how does GH binding activate JAK2. In: Annual Scientific Meeting of the Endocrine Society of Australia, Adelaide, Australia, (16-16). 23-26 August, 2015. doi:10.1111/cen.13010
Deplazes, Evelyne, Henriques, Sonia Troeira, King, Glenn F., Craik, David J., Mark, Alan E. and Schroeder, Christina I. (2016). Membrane-binding properties of gating-modifier and pore blocking toxins: membrane interaction is not a prerequisite for modification of channel gating. In: 60th Annual Meeting of the Biophysical-Society, Los Angeles, United States, (29A-29A). February 27- March 2 2016. doi:10.1016/j.bpj.2015.11.220
Corbett, Michael, Poger, David and Mark, Alan E. (2016). A cytokine receptor revolution: activation of the Type-I Cytokine Receptors via protomer rotation. In: 60th Annual Meeting of the Biophysical Society, Los Angeles, CA, United States, (592A-592A). 27 February- 2 March 2016.
Deplazes, Evelyne, Davies, Josephine, Bonvin, Alexandre M. J. J. and Mark, Alan E. (2016). On the Combination of Restraint-Driven Docking of Flexible Peptides to Ion Channels - Lessons Learnt from the Complex Formed by the Spider Venom PcTx1 and the Acid Sensing Ion Channel1. In: 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, United States, (536A-536A). February 27- March 2 2016.
Malde, Alpeshkumar K. and Mark, Alan E. (2015). Validation of ligands in X-ray crystal structures. In: , , (117-117). . doi:10.1080/07391102.2015.1032811
Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2015). Validation and development of the force field parameters for drug and drug-like molecules. In: Biophysical Society 59th Annual Meeting, Baltimore, United States, (158A-158A). February 7-11, 2015. doi:10.1016/j.bpj.2014.11.869
Malde, Alpeshkumar K. and Mark, Alan E. (2015). 179 Validation of ligands in X-ray crystal structures. In: Book of Abstracts. Albany 2015: The 19th Conversation. The 19th Conversation, Albany/State University of New York, (117-117). 9-13 June 2015. doi:10.1080/07391102.2015.1032816
Condic-Jurkic, K., Subramanian, N., Mark, A. E. and O'Mara, M. (2015). Insights into the operations of a promiscuous drug trafficker: The story of P-glycoprotein. In: 10th European Biophysical Societies Association (EBSA) European Biophysics Congress, Dresden, Germany, (S164-S164). 18-22 July 2015. doi:10.1007/s00249-015-1045-6
Koziara, K. B., Stroet, M., Malde, A. K. and Mark, A. E. (2015). Validation and development of force field parameters for drug and drug-like molecules. In: 10th European Biophysical Societies Association (EBSA) European Biophysics Congress, Dresden Germany, (S160-S160). 18-22 July 2015.
Brooks, Andrew J, Chhabra, Yash, Abankwa, Daniel, O’Mara, Megan, Dai, Wei, Gardon, Olivier, Tunny, Kathryn A., Blucher, Kristopher M., Morton, Craig J., Parker, Michael W., Sierecki, Emma, Gambin, Yann, Guillermo A. Gomez, Alexandrov, Kirill Kirill, Doxastakis, Manolis, Mark, Alan E. and Waters, Michael J. (2014). A new cytokine receptor activation paradigm: Activation of JAK2 by the growth hormone receptor. In: SI: 2014 ICIS Abstract Issue, ICIS Conference. 2nd Annual Meeting of the International Cytokine and Interferon Society (ICIS), Melbourne, VIC Australia, (22-22). 26 - 29 October 2014. doi:10.1016/j.cyto.2014.07.227
Mark, Alan E. (2013). Understanding the Induction and Stabilization of Transmembrane Pores by Peptides. In: Abstracts of the 57th Annual Meeting of the Biophysical Society. 57th Annual Meeting of the Biophysical Society, Philadelphia Pa, (601A-601A). 02-06 February 2013. doi:10.1016/j.bpj.2012.11.3335
Canzar, Stefan, El-Kebir, Mohammed, Pool, Rene, Elbassioni, Khaled, Malde, Alpesh K., Mark, Alan E., Geerke, Daan P., Stougie, Leen and Klau, Gunnar W. (2012). Charge group partitioning in biomolecular simulation. In: Benny Chor, Proceedings: 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012. 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, (29-43). 21 - 24 April 2012. doi:10.1007/978-3-642-29627-7_3
Yennamalli, RM, Kobe, B, Mark, AE, Young, PR and Subbarao, N (2009). Dengue viral envelope protein and histidine protonation. In: Indian Journal of Virology. XVIII National Conference of Indian Virological Society, Post Graduate Institute of Medical Education and Research, Chandigarh, India., (29-29). 11–13 December 2008.
Sengupta, D., Leontiadou, H., Mark, A. E. and Marrink, S. J. (2007). Molecular dynamics simulations of toroidal pores formed by antimicrobial peptides. In: Biophysical Journal: Annual Meeting Abstracts Issues. Biophysical Society 51st Annual Meeting, Bethesda, MA, (545A-545A). 3-7 March 2007.
Kampmann, T., Muller,, Robinson, J., Mark, A, Young, P R and Kobe, B (2006). The mechanism of vira membrane fusion and identification of novel antiviral lead compounds. In: 31st Lorne Conference on Protein Structure & Function. 31st Lorne Conference on Protein Structure & Function, Lorne, Victoria, Australia, (Abstract). 5-9 Feb, 2006.
de Vries, AH, Knecht, V, Yefimov, S, Mark, AE and Marrink, SI (2005). Simulations of phase transformations of lipid-water mixtures by molecular dynamics. In: Abstracts of Papers of the American Chemical Society. 230th National Meeting of the American-Chemical-Society, Washington Dc, (U1241-U1241). Aug 28-Sep 01, 2005.
Kovalskyy, DB, Dubina, VM, Mark, AE and Kornelyuk, AI (2005). Effect of distal mutations on the molecular dynamics of the HIV-1 protease. In: Febs Journal. IUBMB 50th Anniversary Symposium, Budapest Hungary, (143-143). Jul 02-07, 2005.
Marrink, SJ and Mark, AE (2005). Coarse grained simulation of phase transitions of lipid membranes. In: Biophysical Journal. 49th Annual Meeting of the Biopysical-Society, Long Beach Ca, (384A-384A). Feb 12-16, 2005.
Kampmann, T., Muller, D. A., Robinson, J., Mark, A., Young, P. R. and Kobe, B. (2005). A structural model for low pH mediated viral fusion: The role of histidine protonation. In: 3rd Australian Virology Group Meeting. 3rd Australian Virology Group Meeting, Phillip Island, (Abstract). 9-12 Dec, 2005.
Knecht, V, Marrink, SJ and Mark, AE (2005). Simulation studies of self-organization in lipid systems. In: Biophysical Journal. 49th Annual Meeting of the Biopysical-Society, Long Beach Ca, (384A-384A). Feb 12-16, 2005.
Mark, AE and Vangunsteren, WF (1995). Free energy calculations in drug design: A practical guide. In: New Perspectives in Drug Design. 9th International Round Table of the Rhone-Poulenc-Rorer-Foundation on New Perspectives in Drug Design, Turnberry Scotland, (185-200). Apr, 1994.
Vangunsteren, WF, Brunne, RM, Mark, AE and Vanhelden, SP (1992). Computer-Simulation of Biomolecules - Comparison with Experimental-Data. In: BERTRAN, J, Molecular Aspects of Biotechnology : Computational Models and Theories. Nato Advanced Research Workshop On the Role of Computational Models and Theories in Biotechnology, Sant Feliu Guixols Spain, (105-122). Jun 13-19, 1991.
Vanhelden, SP, Vaneijck, BP, Mark, AE, Vangunsteren, WF and Janssen, Lhm (1992). Molecular-Dynamics and Free-Energy Perturbation Calculations On Complexes of Alpha-Cyclodextrins with P-Substituted Phenols, a Comparison Between Experiment and Simulation. In: Hedges, AR, Minutes of the Sixth International Symposium On Cyclodextrins. 6Th International Symp On Cyclodextrins, Chicago Il, (170-175). Apr 21-24, 1992.