OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
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J. Comput. Aided Mol. Des., August, 2023
PyThinFilm: Automated Molecular Dynamics Simulation Protocols for the Generation of Thin Film Morphologies.
J. Chem. Inf. Model., 2023
Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations.
J. Chem. Inf. Model., 2019
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.
Algorithms Mol. Biol., 2019
Effect of Binding on Enantioselectivity of Epoxide Hydrolase.
J. Chem. Inf. Model., 2018
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018
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., 2016
Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques.
J. Chem. Inf. Model., 2015
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
J. Comput. Aided Mol. Des., 2014
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol., 2013
Charge Group Partitioning in Biomolecular Simulation.
Proceedings of the Research in Computational Molecular Biology, 2012
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes.
J. Comput. Aided Mol. Des., 2011
A new force field for simulating phosphatidylcholine bilayers.
J. Comput. Chem., 2010
Basic ingredients of free energy calculations: A review.
J. Comput. Chem., 2010
Probing the free energy landscape of the FBP28WW domain using multiple techniques.
J. Comput. Chem., 2009
The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.
J. Comput. Chem., 2006
GROMACS: Fast, flexible, and free.
J. Comput. Chem., 2005
Incorporating the effect of ionic strength in free energy calculations using explicit ions.
J. Comput. Chem., 2005
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., 2004
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., 2003
Calculation of the free energy of solvation for neutral analogs of amino acid side chains.
J. Comput. Chem., 2002
Estimating relative free energies from a single ensemble: Hydration free energies.
J. Comput. Chem., 1999
Estimating Relative Free Energies from a Single Simulation of the Initial State.
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999
Parametrization of aliphatic CHn united atoms of GROMOS96 force field.
J. Comput. Chem., 1998
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes.
J. Comput. Aided Mol. Des., 1993