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)

Parametrization of aliphatic CHn united atoms of GROMOS96 force field. - Xavier Daura; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 1998)

Estimating Relative Free Energies from a Single Simulation of the Initial State. - Alan E. Mark; Heiko Schäfer; Haiyan Liu; Wilfred F. van Gunsteren (Computational Molecular Dynamics, 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)

Calculation of the free energy of solvation for neutral analogs of amino acid side chains. - Alessandra Villa; Alan E. Mark (J. Comput. Chem., 2002)

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)

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)

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)

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)

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)

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)

Basic ingredients of free energy calculations: A review. - Clara D. Christ; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 2010)

A new force field for simulating phosphatidylcholine bilayers. - David Poger; Wilfred F. van Gunsteren; Alan E. Mark (J. Comput. Chem., 2010)

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)

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 (RECOMB, 2012)

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)

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)

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)

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)

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 (WABI, 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)

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)

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)

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)

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; et al. (J. Comput. Aided Mol. Des., 2023)