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2013 Journal Article Charge group partitioning in biomolecular simulationCanzar, 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 |
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2013 Journal Article Vancomycin: ligand recognition, dimerization and super-complex formationJia, 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 |
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2013 Journal Article 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))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 |
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2013 Book Chapter Study of proteins and peptides at interfaces by molecular dynamics simulation techniquesPoger, David and Mark, Alan E. (2013). Study of proteins and peptides at interfaces by molecular dynamics simulation techniques. Proteins in solution and at interfaces: methods and applications in biotechnology and materials science. (pp. 291-313) edited by Juan M Ruso and Angel Pineiro. Hoboken NJ, United States: John Wiley & Sons, Inc.. doi: 10.1002/9781118523063.ch14 |
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2013 Conference Publication Understanding the Induction and Stabilization of Transmembrane Pores by PeptidesMark, Alan E. (2013). Understanding the Induction and Stabilization of Transmembrane Pores by Peptides. 57th Annual Meeting of the Biophysical Society, Philadelphia Pa, 02-06 February 2013. Maryland Heights, MO United States: Cell Press. doi: 10.1016/j.bpj.2012.11.3335 |
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2012 Journal Article Lipid bilayers: the effect of force field on ordering and dynamicsPoger, 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 |
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2012 Journal Article Molecular dynamics simulations of the interactions of DMSO with DPPC and DOPC phospholipid membranesHughes, 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 |
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2012 Journal Article Wilfred van Gunsteren: 35 years of biomolecular simulationHuenenberger, 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 |
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2012 Journal Article Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo modelsFan, 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 |
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2012 Journal Article Molecular dynamics unlocks atomic level self-assembly of the exopolysaccharide matrix of water-treatment granular biofilmsSeviour, 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 |
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2012 Journal Article The effect of environment on the structure of a membrane protein: P-glycoprotein under physiological conditionsO’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 |
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2012 Journal Article Missing fragments: Detecting cooperative binding in fragment-based drug designNair, 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 |
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2012 Conference Publication Charge group partitioning in biomolecular simulationCanzar, 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. 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, Barcelona, Spain, 21 - 24 April 2012. Heidelberg, Germany: Springer. doi: 10.1007/978-3-642-29627-7_3 |
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2011 Journal Article An automated force field topology builder (ATB) and repository: Version 1.0Malde, 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 |
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2011 Journal Article The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid IIJia, 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 |
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2011 Journal Article Protein a-turns recreated in structurally stable small moleculesHoang, 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 |
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2011 Journal Article A dynamic pharmacophore drives the interaction between psalmotoxin-1 and the putative drug target acid-sensing ion channel 1aSaez, 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 |
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2011 Journal Article Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitorsRiniker, 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, 024105.1-024105.13. doi: 10.1063/1.3604534 |
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2011 Journal Article Definition and testing of the GROMOS force-field versions 54A7 and 54B7Schmid, 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 |
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2011 Journal Article Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT)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 |
