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Alan E. Mark
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2020 – today
- 2023
- [j22]Martin Stroet
, Bertrand Caron, Martin S. Engler
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37(8): 357-371 (2023) - [j21]Martin Stroet
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. J. Chem. Inf. Model. 63(1): 2-8 (2023)
2010 – 2019
- 2019
- [j20]Martin S. Engler
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms Mol. Biol. 14(1): 1:1-1:10 (2019) - [j19]Nandhitha Subramanian
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. J. Chem. Inf. Model. 59(5): 2287-2298 (2019) - 2018
- [j18]Julian Zaugg
Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J. Chem. Inf. Model. 58(3): 630-640 (2018) - [c2]Martin S. Engler
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. WABI 2018: 16:1-16:13 - 2016
- [j17]Evelyne Deplazes
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. J. Chem. Inf. Model. 56(1): 127-138 (2016) - 2015
- [j16]Nandhitha Subramanian
Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. J. Chem. Inf. Model. 55(6): 1202-1217 (2015) - 2014
- [j15]Katarzyna B. Koziara, Martin Stroet
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J. Comput. Aided Mol. Des. 28(3): 221-233 (2014) - 2013
- [j14]Stefan Canzar
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20(3): 188-198 (2013) - 2012
- [c1]Stefan Canzar
Charge Group Partitioning in Biomolecular Simulation. RECOMB 2012: 29-43 - 2011
- [j13]Alpeshkumar K. Malde
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J. Comput. Aided Mol. Des. 25(1): 1-12 (2011) - 2010
- [j12]David Poger
A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. 31(6): 1117-1125 (2010) - [j11]Clara D. Christ, Alan E. Mark
Basic ingredients of free energy calculations: A review. J. Comput. Chem. 31(8): 1569-1582 (2010)
2000 – 2009
- 2009
- [j10]Xavier Periole
Probing the free energy landscape of the FBP28WW domain using multiple techniques. J. Comput. Chem. 30(7): 1059-1068 (2009) - 2006
- [j9]Tsjerk A. Wassenaar
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. J. Comput. Chem. 27(3): 316-325 (2006) - 2005
- [j8]Serena Donnini, Alan E. Mark, André H. Juffer
Incorporating the effect of ionic strength in free energy calculations using explicit ions. J. Comput. Chem. 26(2): 115-122 (2005) - [j7]David van der Spoel
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26(16): 1701-1718 (2005) - 2004
- [j6]Chris Oostenbrink
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25(13): 1656-1676 (2004) - 2003
- [j5]Alessandra Villa, Ronen Zangi, Gilles Pieffet, Alan E. Mark:
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. J. Comput. Aided Mol. Des. 17(10): 673-686 (2003) - 2002
- [j4]Alessandra Villa
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J. Comput. Chem. 23(5): 548-553 (2002)
1990 – 1999
- 1999
- [j3]Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark:
Estimating relative free energies from a single ensemble: Hydration free energies. J. Comput. Chem. 20(15): 1604-1617 (1999) - [p1]Alan E. Mark, Heiko Schäfer, Haiyan Liu
Estimating Relative Free Energies from a Single Simulation of the Initial State. Computational Molecular Dynamics 1999: 149-162 - [e1]Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel:
Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering 4, Springer 1999, ISBN 978-3-540-63242-9 - 1998
- [j2]Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren:
Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19(5): 535-547 (1998) - 1993
- [j1]Paul R. Gerber, Alan E. Mark, Wilfred F. van Gunsteren:
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. J. Comput. Aided Mol. Des. 7(3): 305-323 (1993)
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