Alan E. Mark

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 7

Top Topics

Drosophila Melanogaster

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Comput. Biol.

Publications

Martin Stroet, Stephen Sanderson, Audrey V. Sanzogni, Sharif Nada, Thomas Lee, Bertrand Caron, Alan E. Mark, Paul L. Burn
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies. J. Chem. Inf. Model. 63 (1) (2023)
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
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37 (8) (2023)
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms Mol. Biol. 14 (1) (2019)
Nandhitha Subramanian, Alexandra Schumann-Gillett, Alan E. Mark, Megan L. O'Mara
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. J. Chem. Inf. Model. 59 (5) (2019)
Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde
Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J. Chem. Inf. Model. 58 (3) (2018)
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. WABI (2018)
Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark
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) (2016)
Nandhitha Subramanian, Karmen Condic-Jurkic, Alan E. Mark, Megan L. O'Mara
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) (2015)
Katarzyna B. Koziara, Martin Stroet, Alpeshkumar K. Malde, Alan E. Mark
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J. Comput. Aided Mol. Des. 28 (3) (2014)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20 (3) (2013)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. RECOMB (2012)
Alpeshkumar K. Malde, Alan E. Mark
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes. J. Comput. Aided Mol. Des. 25 (1) (2011)
David Poger, Wilfred F. van Gunsteren, Alan E. Mark
A new force field for simulating phosphatidylcholine bilayers. J. Comput. Chem. 31 (6) (2010)
Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren
Basic ingredients of free energy calculations: A review. J. Comput. Chem. 31 (8) (2010)
Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci
Probing the free energy landscape of the FBP28WW domain using multiple techniques. J. Comput. Chem. 30 (7) (2009)
Tsjerk A. Wassenaar, Alan E. Mark
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions. J. Comput. Chem. 27 (3) (2006)
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26 (16) (2005)
Serena Donnini, Alan E. Mark, André H. Juffer, Alessandra Villa
Incorporating the effect of ionic strength in free energy calculations using explicit ions. J. Comput. Chem. 26 (2) (2005)
Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren
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) (2004)
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) (2003)
Alessandra Villa, Alan E. Mark
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J. Comput. Chem. 23 (5) (2002)
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) (1999)
Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren
Parametrization of aliphatic CHn united atoms of GROMOS96 force field. J. Comput. Chem. 19 (5) (1998)
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) (1993)