Alan E. Mark

According to our database, Alan E. Mark authored at least 25 papers between 1993 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.

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

J. Comput. Aided Mol. Des., August, 2023

PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies.

Martin Stroet, Stephen Sanderson, Audrey V. Sanzogni, Sharif Nada, Thomas Lee, Bertrand Caron, Alan E. Mark, Paul L. Burn

J. Chem. Inf. Model., 2023

2019

Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations.

Nandhitha Subramanian, Alexandra Schumann-Gillett, Alan E. Mark, Megan L. O'Mara

J. Chem. Inf. Model., 2019

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.

Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau

Algorithms Mol. Biol., 2019

2018

Effect of Binding on Enantioselectivity of Epoxide Hydrolase.

Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde

J. Chem. Inf. Model., 2018

Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.

Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

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.

Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark

J. Chem. Inf. Model., 2016

2015

Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques.

Nandhitha Subramanian, Karmen Condic-Jurkic, Alan E. Mark, Megan L. O'Mara

J. Chem. Inf. Model., 2015

2014

Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.

Katarzyna B. Koziara, Martin Stroet, Alpeshkumar K. Malde, Alan E. Mark

J. Comput. Aided Mol. Des., 2014

2013

Charge Group Partitioning in Biomolecular Simulation.

Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau

J. Comput. Biol., 2013

2012

Charge Group Partitioning in Biomolecular Simulation.

Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau

Proceedings of the Research in Computational Molecular Biology, 2012

2011

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.

Alpeshkumar K. Malde, Alan E. Mark

J. Comput. Aided Mol. Des., 2011

2010

A new force field for simulating phosphatidylcholine bilayers.

David Poger, Wilfred F. van Gunsteren, Alan E. Mark

J. Comput. Chem., 2010

Basic ingredients of free energy calculations: A review.

Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren

J. Comput. Chem., 2010

2009

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci

J. Comput. Chem., 2009

2006

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.

Tsjerk A. Wassenaar, Alan E. Mark

J. Comput. Chem., 2006

2005

GROMACS: Fast, flexible, and free.

David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen

J. Comput. Chem., 2005

Incorporating the effect of ionic strength in free energy calculations using explicit ions.

Serena Donnini, Alan E. Mark, André H. Juffer, Alessandra Villa

J. Comput. Chem., 2005

2004

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.

Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren

J. Comput. Chem., 2004

2003

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin.

Alessandra Villa, Ronen Zangi, Gilles Pieffet, Alan E. Mark

J. Comput. Aided Mol. Des., 2003

2002

Calculation of the free energy of solvation for neutral analogs of amino acid side chains.

Alessandra Villa, Alan E. Mark

J. Comput. Chem., 2002

1999

Estimating relative free energies from a single ensemble: Hydration free energies.

Heiko Schäfer, Wilfred F. van Gunsteren, Alan E. Mark

J. Comput. Chem., 1999

Estimating Relative Free Energies from a Single Simulation of the Initial State.

Alan E. Mark, Heiko Schäfer, Haiyan Liu, Wilfred F. van Gunsteren

Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999

1998

Parametrization of aliphatic CHn united atoms of GROMOS96 force field.

Xavier Daura, Alan E. Mark, Wilfred F. van Gunsteren

J. Comput. Chem., 1998

1993

An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes.

Paul R. Gerber, Alan E. Mark, Wilfred F. van Gunsteren

J. Comput. Aided Mol. Des., 1993