Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
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Title
Computationally predicting binding affinity in protein–ligand complexes: free energy-based simulations and machine learning-based scoring functions
Authors
Keywords
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-05-08
DOI
10.1093/bib/bbaa107
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Related references
Note: Only part of the references are listed.- DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity
- (2019) Haiping Zhang et al. PeerJ
- Ligand Binding Pathways and Conformational Transitions of the HIV Protease
- (2018) Yinglong Miao et al. BIOCHEMISTRY
- Development and evaluation of a deep learning model for protein–ligand binding affinity prediction
- (2018) Marta M Stepniewska-Dziubinska et al. BIOINFORMATICS
- OUP accepted manuscript
- (2018) BIOINFORMATICS
- Development of a machine-learning model to predict Gibbs free energy of binding for protein-ligand complexes
- (2018) Gabriela Bitencourt-Ferreira et al. BIOPHYSICAL CHEMISTRY
- Simulations meet machine learning in structural biology
- (2018) Adrià Pérez et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
- (2018) José Jiménez et al. Journal of Chemical Information and Modeling
- Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies
- (2018) Xiao Liu et al. Journal of Chemical Theory and Computation
- MoleculeNet: a benchmark for molecular machine learning
- (2018) Zhenqin Wu et al. Chemical Science
- A machine learning approach towards the prediction of protein–ligand binding affinity based on fundamental molecular properties
- (2018) Indra Kundu et al. RSC Advances
- Development of a Protein-Ligand Extended Connectivity (PLEC) fingerprint and its application for binding affinity predictions
- (2018) Maciej Wójcikowski et al. BIOINFORMATICS
- CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma
- (2016) Heather A. Carlson et al. Journal of Chemical Information and Modeling
- Selectivity profile of afatinib for EGFR-mutated non-small-cell lung cancer
- (2016) Debby D. Wang et al. Molecular BioSystems
- Accurate calculation of the absolute free energy of binding for drug molecules
- (2016) Matteo Aldeghi et al. Chemical Science
- EGFR Mutant Structural Database: computationally predicted 3D structures and the corresponding binding free energies with gefitinib and erlotinib
- (2015) Lichun Ma et al. BMC BIOINFORMATICS
- Improving the LIE Method for Binding Free Energy Calculations of Protein–Ligand Complexes
- (2015) Williams E. Miranda et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
- (2015) Richard D. Smith 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
- ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
- (2015) James A. Maier 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
- BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
- (2015) Michael K. Gilson et al. NUCLEIC ACIDS RESEARCH
- Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis
- (2014) Jing Tang et al. Journal of Chemical Information and Modeling
- Structural Protein–Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study
- (2014) C. Da et al. Journal of Chemical Information and Modeling
- Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes
- (2014) Douglas E.V. Pires et al. NUCLEIC ACIDS RESEARCH
- Scoring Functions for Prediction of Protein-Ligand Interactions
- (2013) Jui-Chih Wang et al. CURRENT PHARMACEUTICAL DESIGN
- Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor
- (2013) Qian Liu et al. Journal of Chemical Information and Modeling
- ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions
- (2013) Guo-Bo Li et al. Journal of Chemical Information and Modeling
- SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes
- (2013) David Zilian et al. Journal of Chemical Information and Modeling
- CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys
- (2013) James B. Dunbar et al. Journal of Chemical Information and Modeling
- Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
- (2012) Lianqing Zheng et al. Journal of Chemical Theory and Computation
- Improved Accuracy of Low Affinity Protein–Ligand Equilibrium Dissociation Constants Directly Determined by Electrospray Ionization Mass Spectrometry
- (2012) Lucie Jaquillard et al. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
- An Efficient Computational Method for Calculating Ligand Binding Affinities
- (2012) Atsushi Suenaga et al. PLoS One
- Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding
- (2011) Aldino Viegas et al. JOURNAL OF CHEMICAL EDUCATION
- CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
- (2011) James B. Dunbar et al. Journal of Chemical Information and Modeling
- Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
- (2011) Liwei Li et al. Journal of Chemical Information and Modeling
- Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
- (2011) Lingle Wang et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Comprehensive analysis of kinase inhibitor selectivity
- (2011) Mindy I Davis et al. NATURE BIOTECHNOLOGY
- Umbrella sampling
- (2011) Johannes Kästner Wiley Interdisciplinary Reviews-Computational Molecular Science
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- CSCORE: A SIMPLE YET EFFECTIVE SCORING FUNCTION FOR PROTEIN–LIGAND BINDING AFFINITY PREDICTION USING MODIFIED CMAC LEARNING ARCHITECTURE
- (2011) XUCHANG OUYANG et al. Journal of Bioinformatics and Computational Biology
- A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
- (2010) Pedro J. Ballester et al. BIOINFORMATICS
- Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
- (2010) Sourav Das et al. Journal of Chemical Information and Modeling
- Extended-Connectivity Fingerprints
- (2010) David Rogers et al. Journal of Chemical Information and Modeling
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics
- (2010) Justin A. Lemkul et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
- (2010) Sheng-You Huang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- λ-Dynamics free energy simulation methods
- (2009) Jennifer L. Knight et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water
- (2009) Halvor S. Hansen et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Distance Dependent Scoring Function for Describing Protein−Ligand Intermolecular Interactions
- (2008) Natalia Artemenko Journal of Chemical Information and Modeling
- Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
- (2008) William L. Jorgensen et al. Journal of Chemical Theory and Computation
- A novel method for protein-ligand binding affinity prediction and the related descriptors exploration
- (2008) Shuyan Li et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Calculation of protein-ligand binding free energy by using a polarizable potential
- (2008) D. Jiao et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
- (2008) Christoph A. Sotriffer et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Predicting Drug-Resistant Mutations of HIV Protease
- (2007) Hiroshi Ishikita et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
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