4.7 Article

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

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

Chuan Tian et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Medicinal

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

Christina E. M. Schindler et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Chemistry, Physical

Advancing Free-Energy Calculations of Metalloenzymes in Drug Discovery via Implementation of LFMM Potentials

Steven Dajnowicz et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

Gregory A. Ross et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

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

Katarina Roos et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Medicinal

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics

Haoyu S. Yu et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)

Article Chemistry, Medicinal

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Fang-Yu Lin et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)

Article Multidisciplinary Sciences

Developing a molecular dynamics force field for both folded and disordered protein states

Paul Robustelli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Article Multidisciplinary Sciences

How well do force fields capture the strength of salt bridges in proteins?

Mustapha Carab Ahmed et al.

Article Chemistry, Physical

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

Wei Chen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Chemistry, Physical

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

Lingle Wang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Article Biochemical Research Methods

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

Article Chemistry, Medicinal

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

Bernd Kuhn et al.

JOURNAL OF MEDICINAL CHEMISTRY (2017)

Article Chemistry, Physical

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization

Xin Cindy Yan et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2017)

Article Chemistry, Multidisciplinary

Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?

Payal Chatterjee et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Review Chemistry, Multidisciplinary

Advancing Drug Discovery through Enhanced Free Energy Calculations

Robert Abel et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

Article Biochemistry & Molecular Biology

Accelerating drug discovery through tight integration of expert molecular design and predictive scoring

Robert Abel et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)

Article Chemistry, Physical

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

Edward Harder et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Medicinal

Application of Free Energy Perturbation for the Design of BACE1 Inhibitors

Myriam Ciordia et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Chemistry, Physical

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

Karl T. Debiec et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Multidisciplinary

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

Eelke B. Lenselink et al.

ACS OMEGA (2016)

Article Chemistry, Physical

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

Michael J. Robertson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Medicinal

A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design

Brett R. Beno et al.

JOURNAL OF MEDICINAL CHEMISTRY (2015)

Article Chemistry, Physical

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

Stefano Piana et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Chemistry, Medicinal

Pyrido[4,3-e][1,2,4]triazolo[4,3-a]pyrazines as Selective, Brain Penetrant Phosphodiesterase 2 (PDE2) Inhibitors

Frederik J. R. Rombouts et al.

ACS MEDICINAL CHEMISTRY LETTERS (2015)

Article Chemistry, Physical

Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

Robert B. Best et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields

Karl T. Debiec et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Article Chemistry, Physical

Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents

William L. Jorgensen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Biochemistry & Molecular Biology

Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation

Dmitry Lupyan et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)

Article Chemistry, Physical

Optimizing Solute-Water van der Waals Interactions To Reproduce Solvation Free Energies

Paul S. Nerenberg et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

Article Chemistry, Medicinal

Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode

Xiaohua Huang et al.

ACS MEDICINAL CHEMISTRY LETTERS (2012)

Article Chemistry, Physical

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

David L. Mobley et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Article Biochemistry & Molecular Biology

More than a Simple Lipophilic Contact: A Detailed Thermodynamic Analysis of Nonbasic Residues in the S1 Pocket of Thrombin

Bernhard Baum et al.

JOURNAL OF MOLECULAR BIOLOGY (2009)

Review Chemistry, Medicinal

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Ken A. Brameld et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)

Article Biochemistry & Molecular Biology

pK values of the ionizable groups of proteins

RL Thurlkill et al.

PROTEIN SCIENCE (2006)

Review Biochemistry & Molecular Biology

Polarizable force fields

TA Halgren et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)