LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

(2017) Leela S. Dodda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling

(2015) Leela S. Dodda et al.   Journal of Chemical Theory and Computation

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered

(2014) J. Peter Guthrie   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

JSME: a free molecule editor in JavaScript

(2013) Bruno Bienfait et al.   Journal of Cheminformatics

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

A Toolkit for the Analysis of Free-Energy Perturbation Calculations

(2012) Peng Liu et al.   Journal of Chemical Theory and Computation

Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases

(2012) Aleksandr V. Marenich et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

MATCH: An atom-typing toolset for molecular mechanics force fields

(2011) Joseph D. Yesselman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computer Review of ChemDraw Ultra 12.0 ChemDraw Ultra 12.0 . CambridgeSoft , 100 Cambridge Park Drive, Cambridge, MA 02140 . www.cambridgesoft.com . See Web site for full pricing information.

(2011) Kimberley R. Cousins   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMMing: A New, Flexible Web Portal for CHARMM

(2008) Benjamin T. Miller et al.   Journal of Chemical Information and Modeling

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY