Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
出版年份 2021 全文链接
标题
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
作者
关键词
-
出版物
Journal of Chemical Theory and Computation
Volume 17, Issue 3, Pages 2000-2010
出版商
American Chemical Society (ACS)
发表日期
2021-02-13
DOI
10.1021/acs.jctc.0c01184
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
- (2020) Ryan E. Pavlovicz et al. PLoS Computational Biology
- OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules
- (2019) Katarina Roos et al. Journal of Chemical Theory and Computation
- Optimized Lennard-Jones Parameters for Druglike Small Molecules
- (2018) Eliot Boulanger et al. Journal of Chemical Theory and Computation
- The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
- (2017) Rebecca F. Alford et al. Journal of Chemical Theory and Computation
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
- (2017) Minkyung Baek et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Can computed crystal energy landscapes help understand pharmaceutical solids?
- (2016) Sarah L. Price et al. CHEMICAL COMMUNICATIONS
- An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
- (2016) Justin A. Lemkul et al. CHEMICAL REVIEWS
- Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
- (2016) Hahnbeom Park et al. Journal of Chemical Theory and Computation
- Overview of the SAMPL5 host–guest challenge: Are we doing better?
- (2016) Jian Yin et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods
- (2016) Anders Broo et al. Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials
- Report on the sixth blind test of organic crystal structure prediction methods
- (2016) Anthony M. Reilly et al. Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials
- The Cambridge Structural Database
- (2016) Colin R. Groom et al. Acta Crystallographica Section B-Structural Science Crystal Engineering and Materials
- A New, Improved Hybrid Scoring Function for Molecular Docking and Scoring Based on AutoDock and AutoDock Vina
- (2015) Vsevolod Yu Tanchuk et al. Chemical Biology & Drug Design
- Facts and fictions about polymorphism
- (2015) Aurora J. Cruz-Cabeza et al. CHEMICAL SOCIETY REVIEWS
- FlexAID: Revisiting Docking on Non-Native-Complex Structures
- (2015) Francis Gaudreault et al. Journal of Chemical Information and Modeling
- 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
- 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
- The Cambridge Structural Database in Retrospect and Prospect
- (2014) Colin R. Groom et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space
- (2014) Sofie Jakobsen et al. Journal of Chemical Theory and Computation
- FreeSolv: a database of experimental and calculated hydration free energies, with input files
- (2014) David L. Mobley et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
- (2014) Sergio Ruiz-Carmona et al. PLoS Computational Biology
- Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields
- (2013) Markus K. Dahlgren et al. Journal of Chemical Information and Modeling
- 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
- Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
- (2012) Matthew P. Repasky et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Surflex-Dock: Docking benchmarks and real-world application
- (2012) Russell Spitzer et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test
- (2012) John W. Liebeschuetz et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- An Efficient Computational Method for Calculating Ligand Binding Affinities
- (2012) Atsushi Suenaga et al. PLoS One
- On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
- (2012) L. Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of Vaporization
- (2011) Junmei Wang et al. Journal of Chemical Theory and Computation
- Modeling Symmetric Macromolecular Structures in Rosetta3
- (2011) Frank DiMaio et al. PLoS One
- Confab - Systematic generation of diverse low-energy conformers
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
- (2009) Oliver Korb et al. Journal of Chemical Information and Modeling
- High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
- (2009) Noriaki Okimoto et al. PLoS Computational Biology
- Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis
- (2008) Ken A. Brameld et al. Journal of Chemical Information and Modeling
- Protein−Ligand Docking against Non-Native Protein Conformers
- (2008) Marcel L. Verdonk et al. Journal of Chemical Information and Modeling
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