Alan E. Mark

发表

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, 2003, J. Comput. Aided Mol. Des..

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

Chris Oostenbrink, Wilfred F. van Gunsteren, Alessandra Villa, 2004, J. Comput. Chem..

Basic ingredients of free energy calculations: A review

Wilfred F. van Gunsteren, Alan E. Mark, Clara D. Christ, 2009, J. Comput. Chem..

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

Alessandra Villa, Alan E. Mark, A. Mark, 2002, J. Comput. Chem..

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

Alan E. Mark, Haiyan Liu, Heiko Schäfer, 1999, Computational Molecular Dynamics.

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

Gunnar W. Klau, Bertrand Caron, Daan P. Geerke, 2018, WABI.

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

Wilfred F. van Gunsteren, Alan E. Mark, Paul R. Gerber, 1993, J. Comput. Aided Mol. Des..

Charge Group Partitioning in Biomolecular Simulation

Khaled M. Elbassioni, Leen Stougie, Gunnar W. Klau, 2012, RECOMB.

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

Alan E. Mark, Alpeshkumar K. Malde, A. Mark, 2011, J. Comput. Aided Mol. Des..

The GROMOS96 benchmarks for molecular simulation

Alexandre M. J. J. Bonvin, Wilfred F. van Gunsteren, Alan E. Mark, 2000 .

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

Gunnar W. Klau, Bertrand Caron, Daan P. Geerke, 2019, Algorithms for Molecular Biology.

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

Wilfred F. van Gunsteren, Xavier Daura, Alan E. Mark, 1998, J. Comput. Chem..

Computational Molecular Dynamics: Challenges, Methods, Ideas: Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modellin

Benedict Leimkuhler, Robert D. Skeel, Sebastian Reich, 1999 .

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

Alan E. Mark, Megan L. O'Mara, Karmen Condic-Jurkic, 2015, J. Chem. Inf. Model..

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

Alexandre M. J. J. Bonvin, Alan E. Mark, Glenn F. King, 2016, J. Chem. Inf. Model..

GROMACS: Fast, flexible, and free

Gerrit Groenhof, Berk Hess, Erik Lindahl, 2005, J. Comput. Chem..

Charge Group Partitioning in Biomolecular Simulation

Khaled M. Elbassioni, Leen Stougie, Gunnar W. Klau, 2013, J. Comput. Biol..

Eppur si Muove (and Yet it Does Move): A Perspective on the Past, Present and Future of Atomistic Simulations in Structural Biology

Alan E. Mark, David E. Hoke, Itamar Kass, 2014 .

A new force field for simulating phosphatidylcholine bilayers

Wilfred F. van Gunsteren, Alan E. Mark, David Poger, 2010, J. Comput. Chem..

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

Alan E. Mark, Alpeshkumar K. Malde, Martin Stroet, 2014, Journal of Computer-Aided Molecular Design.

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

Wilfred F. van Gunsteren, Alan E. Mark, Heiko Schäfer, 1999, J. Comput. Chem..

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

Alessandra Villa, Alan E. Mark, André H. Juffer, 2005, J. Comput. Chem..

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

Alan E. Mark, Emanuele Paci, Xavier Periole, 2009, J. Comput. Chem..

Computer simulation of protein motion

Alan E. Mark, W. F. van Gunsteren, Philippe H. Hünenberger, 1995 .

CONVERGENCE PROPERTIES OF FREE ENERGY CALCULATIONS : ALPHA -CYCLODEXTRIN COMPLEXES AS A CASE STUDY

Wilfred F. van Gunsteren, Alan E. Mark, Steven P. van Helden, 1994 .

Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions

Francesc X. Avilés, Enrique Querol, Xavier Daura, 1996 .

Validation of molecular dynamics simulation

Wilfred F. van Gunsteren, Alan E. Mark, A. Mark, 1998 .

A new 2,2,2-trifluoroethanol model for molecular dynamics simulations

Alan E. Mark, Marco Fioroni, Klaus Burger, 2000 .

GROMOS Force Field

Wilfred F. van Gunsteren, Xavier Daura, Alan E. Mark, 2002 .

New Algorithms for Macromolecular Simulation (Lecture Notes in Computational Science and Engineering)

Tamar Schlick, Benedict Leimkuhler, Ron Elber, 2006 .

Applications of free energy calculations to chemistry and biology

Vijay S. Pande, Thomas Simonson, Christophe Chipot, 2007 .

Absolute entropies from molecular dynamics simulation trajectories

Wilfred F. van Gunsteren, Alan E. Mark, A. Mark, 2000 .

Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State

Alan E. Mark, W. F. van Gunsteren, A. Mark, 1996 .

Bilayer ice and alternate liquid phases of confined water

Ronen Zangi, Alan E. Mark, A. Mark, 2003 .

Dynamic conformations of flavin adenine dinucleotide: Simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics

Alan E. Mark, K. A. Feenstra, H. Berendsen, 2002 .

Computation of free energy

Wilfred F. van Gunsteren, Xavier Daura, Alan E. Mark, 2002 .

Effect of Undulations on Surface Tension in Simulated Bilayers

Alan E. Mark, Siewert J. Marrink, A. Mark, 2001 .

Molecular dynamics simulation of the kinetics of spontaneous micelle formation

Alan E. Mark, Siewert J. Marrink, A. Mark, 2000 .

The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol

Wilfred F. van Gunsteren, Alan E. Mark, Georges Wipff, 2000 .

Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations

Alan E. Mark, Wilfred F. van Gunsteren, Roger M. Brunne, 1993 .

The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action

Rong Chen, Alan E. Mark, A. Mark, 2011, European Biophysics Journal.

The GROMOS96 Manual and User Guide

Alan E. Mark, W. F. van Gunsteren, Philippe H. Hünenberger, 1996 .

Calculation of Relative Free-Energy Via Indirect Pathways

Alan E. Mark, W. F. van Gunsteren, H. Berendsen, 1991 .