Alan E. Mark

26 papers B 1C 1Journal 22
YearRankTypeTitle / Venue / Authors
2023 J jnl
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
J. Comput. Aided Mol. Des.
Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2023 J jnl
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies.
J. Chem. Inf. Model.
Martin Stroet, Stephen Sanderson, Audrey V. Sanzogni, Sharif Nada, Thomas Lee, Bertrand Caron, Alan E. Mark, Paul L. Burn
2019 J jnl
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.
Algorithms Mol. Biol.
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2019 J jnl
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations.
J. Chem. Inf. Model.
Nandhitha Subramanian, Alexandra Schumann-Gillett, Alan E. Mark, Megan L. O'Mara
2018 J jnl
Effect of Binding on Enantioselectivity of Epoxide Hydrolase.
J. Chem. Inf. Model.
Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde
2018 C conf
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.
WABI
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2016 J jnl
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.
Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark
2015 J jnl
Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques.
J. Chem. Inf. Model.
Nandhitha Subramanian, Karmen Condic-Jurkic, Alan E. Mark, Megan L. O'Mara
2014 J jnl
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
J. Comput. Aided Mol. Des.
Katarzyna B. Koziara, Martin Stroet, Alpeshkumar K. Malde, Alan E. Mark
2013 J jnl
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol.
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2012 B conf
Charge Group Partitioning in Biomolecular Simulation.
RECOMB
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2011 J jnl
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.
J. Comput. Aided Mol. Des.
Alpeshkumar K. Malde, Alan E. Mark
2010 J jnl
A new force field for simulating phosphatidylcholine bilayers.
J. Comput. Chem.
David Poger, Wilfred F. van Gunsteren, Alan E. Mark
2010 J jnl
Basic ingredients of free energy calculations: A review.
J. Comput. Chem.
Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren
2009 J jnl
Probing the free energy landscape of the FBP28WW domain using multiple techniques.
J. Comput. Chem.
Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci
2006 J jnl
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
J. Comput. Chem.
Tsjerk A. Wassenaar, Alan E. Mark
2005 J jnl
GROMACS: Fast, flexible, and free.
J. Comput. Chem.
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
2005 J jnl
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
J. Comput. Chem.
Serena Donnini, Alan E. Mark, André H. Juffer, Alessandra Villa
2004 J jnl
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.
Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren
2003 J jnl
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.
Alessandra Villa, Ronen Zangi, Gilles Pieffet, Alan E. Mark
2002 J jnl
Calculation of the free energy of solvation for neutral analogs of amino acid side chains.
J. Comput. Chem.
Alessandra Villa, Alan E. Mark
1999 — book
Computational Molecular Dynamics: Challenges, Methods, Ideas
Computational Molecular Dynamics
Peter Deuflhard, Jan Hermans, Benedict J. Leimkuhler, Alan E. Mark, Sebastian Reich, Robert D. Skeel
1999 — ch.
Estimating Relative Free Energies from a Single Simulation of the Initial State.
Computational Molecular Dynamics
Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred F. van Gunsteren
1999 J jnl
Estimating relative free energies from a single ensemble: Hydration free energies.
J. Comput. Chem.
Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark
1998 J jnl
Parametrization of aliphatic CHn united atoms of GROMOS96 force field.
J. Comput. Chem.
Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren
1993 J jnl
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes.
J. Comput. Aided Mol. Des.
Paul R. Gerber, Alan E. Mark, Wilfred F. van Gunsteren