Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters

(2021) Jordan N. Ehrman et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Psi4 1.4: Open-source software for high-throughput quantum chemistry

(2020) Daniel G. A. Smith et al.   JOURNAL OF CHEMICAL PHYSICS

Rigorous Free Energy Simulations in Virtual Screening

(2020) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Driving torsion scans with wavefront propagation

(2020) Yudong Qiu et al.   JOURNAL OF CHEMICAL PHYSICS

The MolSSI QCA rchive project: An open‐source platform to compute, organize, and share quantum chemistry data

(2020) Daniel G. A. Smith et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

(2019) Katarina Roos et al.   Journal of Chemical Theory and Computation

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

(2019) Joshua T. Horton et al.   Journal of Chemical Information and Modeling

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set

(2018) Jan Řezáč et al.   Journal of Chemical Theory and Computation

Bind3P: Optimization of a Water Model Based on Host–Guest Binding Data

(2018) Jian Yin et al.   Journal of Chemical Theory and Computation

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

(2018) David J. Huggins et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

Overview of the SAMPL6 host–guest binding affinity prediction challenge

(2018) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability

(2017) Robert M. Parrish et al.   Journal of Chemical Theory and Computation

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

(2017) Lee-Ping Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Geometry optimization made simple with translation and rotation coordinates

(2016) Lee-Ping Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

(2016) Ian M. Kenney et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

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

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

Benchmark ab Initio Conformational Energies for the Proteinogenic Amino Acids through Explicitly Correlated Methods. Assessment of Density Functional Methods

(2015) Manoj K. Kesharwani et al.   Journal of Chemical Theory and Computation

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

(2015) Niel M. Henriksen et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

(2015) Kyle A. Beauchamp et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

(2014) David S. Cerutti et al.   Journal of Chemical Theory and Computation

pmx: Automated protein structure and topology generation for alchemical perturbations

(2014) Vytautas Gapsys et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Fixed-Charge Model for Alcohol Polarization in the Condensed Phase, and Its Role in Small Molecule Hydration

(2014) Christopher J. Fennell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Corrected small basis set Hartree-Fock method for large systems

(2013) Rebecca Sure et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ligand Pose and Orientational Sampling in Molecular Docking

(2013) Ryan G. Coleman et al.   PLoS One

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Effect of the damping function in dispersion corrected density functional theory

(2011) Stefan Grimme et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

(2010) Daniel Seeliger et al.   BIOPHYSICAL JOURNAL

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

(2010) Stefan Grimme et al.   JOURNAL OF CHEMICAL PHYSICS

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

(2009) Robert S. Paton et al.   Journal of Chemical Information and Modeling

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Medicinal Chemistry and the Molecular Operating Environment (MOE): Application of QSAR and Molecular Docking to Drug Discovery

(2008) Santiago Vilar et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY