Department of Computational Biological Chemistry
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn | Journal of Computer-Aided Molecular Design
Full article: Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4
Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free ener ... - Physical Chemistry Chemical Physics (RSC Publishing) DOI:10.1039/D1CP00215E
Frontiers | Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool
Validation of the Generalized Force Fields GAFF, CGenFF, OPLS-AA, and PRODRGFF by Testing Against Experimental Osmotic Coefficient Data for Small Drug-Like Molecules | Journal of Chemical Information and Modeling
Protein-ligand complex | Gromacs tutorial | CHARMM forcefield | Molecular dynamics simulation - YouTube
Molecules | Free Full-Text | Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields
Full article: Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4
GitHub - jandom/paramchem: Python scrapper for paramche/cgenff server, small molecule parametrization
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules - Kumar - 2020 - Journal of Computational Chemistry - Wiley Online Library
CGenFF: CHARMM General Force Field — SilcsBio User Guide
CGenFF Server Ligand Penalties - User discussions - GROMACS forums
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules | SpringerLink
How to generate CHARMM force field for GROMACS using CGenFF? | ResearchGate
Problem in file (Broken structure ini.pdb) generated using CGenFF for proceeding in MD Simulation - User discussions - GROMACS forums
CGenFF
NAMD QM/MM (CGenFF) - Adrea's Notebook and Journal
Problem while generating JZ4 Topology with CGenFF - User discussions - GROMACS forums
Protein-Ligand Complex
Assessing the quality of absolute hydration free energies among CHARMMcompatible ligand parameterization schemes
Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field | Journal of Chemical Theory and Computation
Validation of the Generalized Force Fields GAFF, CGenFF, OPLS-AA, and PRODRGFF by Testing Against Experimental Osmotic Coefficient Data for Small Drug-Like Molecules | Journal of Chemical Information and Modeling
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