An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking

Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA)

(2018) Le Zhang et al.   BIOINFORMATICS

Development and evaluation of a deep learning model for protein–ligand binding affinity prediction

(2018) Marta M Stepniewska-Dziubinska et al.   BIOINFORMATICS

Improving classical scoring functions using random forest: The non-additivity of free energy terms’ contributions in binding

(2018) Karim Afifi et al.   Chemical Biology & Drug Design

Development of a Fingerprint-Based Scoring Function for the Prediction of the Binding Mode of Carbonic Anhydrase II Inhibitors

(2018) Giulio Poli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

(2018) Casper Steinmann et al.   Journal of Chemical Theory and Computation

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

(2018) Zixuan Cang et al.   PLoS Computational Biology

Boosted neural networks scoring functions for accurate ligand docking and ranking

(2018) Hossam M. Ashtawy et al.   Journal of Bioinformatics and Computational Biology

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer

(2018) Heather J. Kulik   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein–Ligand Empirical Interaction Components for Virtual Screening

(2017) Yuna Yan et al.   Journal of Chemical Information and Modeling

A Hybrid Knowledge-Based and Empirical Scoring Function for Protein–Ligand Interaction: SMoG2016

(2017) Théau Debroise et al.   Journal of Chemical Information and Modeling

Protein–Ligand Scoring with Convolutional Neural Networks

(2017) Matthew Ragoza et al.   Journal of Chemical Information and Modeling

An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems

(2017) Yoelvis Orozco-Gonzalez et al.   Journal of Chemical Theory and Computation

Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization

(2017) Maria Kadukova et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

(2017) Minkyung Baek et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing

(2017) Gang Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

Using game theory to investigate the epigenetic control mechanisms of embryo development

(2017) Le Zhang et al.   Physics of Life Reviews

EZH2-, CHD4-, and IDH-linked epigenetic perturbation and its association with survival in glioma patients

(2017) Le Zhang et al.   Journal of Molecular Cell Biology

Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function

(2017) Li Zhang et al.   Oncotarget

On-the-Fly QM/MM Docking with Attracting Cavities

(2016) Prasad Chaskar et al.   Journal of Chemical Information and Modeling

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

(2016) Shota Uehara et al.   MOLECULES

Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation

(2016) Le Zhang et al.   Nanoscale

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Machine learning in computational docking

(2015) Mohamed A. Khamis et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes

(2015) Hossam M Ashtawy et al.   BMC BIOINFORMATICS

Classification of Current Scoring Functions

(2015) Jie Liu et al.   Journal of Chemical Information and Modeling

Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets

(2015) Hongjian Li et al.   Molecular Informatics

Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening

(2015) Qurrat Ul Ain et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures

(2014) Jungkap Park et al.   BMC BIOINFORMATICS

Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

(2014) Hongjian Li et al.   BMC BIOINFORMATICS

Finding chemical drugs for genetic diseases

(2014) Hui-Yong Sun et al.   DRUG DISCOVERY TODAY

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function

(2014) Prasad Chaskar et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

(2014) Diogo Santos-Martins et al.   Journal of Chemical Information and Modeling

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

(2014) Sheng-You Huang et al.   NUCLEIC ACIDS RESEARCH

Drug repositioning by structure-based virtual screening

(2013) Dik-Lung Ma et al.   CHEMICAL SOCIETY REVIEWS

A Genetic Algorithm- Back Propagation Artificial Neural Network Model to Quantify the Affinity of Flavonoids Toward P-Glycoprotein

(2013) Jibin Shen et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Scoring Functions for Prediction of Protein-Ligand Interactions

(2013) Jui-Chih Wang et al.   CURRENT PHARMACEUTICAL DESIGN

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap

(2013) Yue Yang et al.   Expert Opinion on Drug Discovery

Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening

(2013) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures

(2013) Bo Ding et al.   Journal of Chemical Information and Modeling

Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein–Ligand Complexes Using Support Vector Machines

(2013) Chaitanya A. K. Koppisetty et al.   Journal of Chemical Information and Modeling

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

Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches

(2013) Huiyong Sun et al.   Journal of Chemical Information and Modeling

Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise

(2013) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints

(2013) Vladimir Chupakhin et al.   Journal of Chemical Information and Modeling

Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction

(2013) Michal Brylinski   Journal of Chemical Information and Modeling

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions

(2013) Zheng Zheng et al.   Journal of Chemical Information and Modeling

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

(2013) Woong-Hee Shin et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review

(2012) Tiejun Cheng et al.   AAPS Journal

Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening

(2012) Bo Ding et al.   Journal of Chemical Information and Modeling

Binding Affinity Prediction for Ligands and Receptors Forming Tautomers and Ionization Species: Inhibition of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK2)

(2012) Senthil Natesan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

(2012) Gregory A. Ross et al.   PLoS One

Ligand Identification Scoring Algorithm (LISA)

(2011) Zheng Zheng et al.   Journal of Chemical Information and Modeling

A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing

(2011) Sarah L. Kinnings et al.   Journal of Chemical Information and Modeling

NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function

(2011) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

(2011) Gerd Neudert et al.   Journal of Chemical Information and Modeling

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

(2011) Stefano Forli et al.   JOURNAL OF MEDICINAL CHEMISTRY

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes

(2010) Jacob D. Durrant et al.   Journal of Chemical Information and Modeling

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

(2010) Sheng-You Huang et al.   Journal of Chemical Information and Modeling

VoteDock: Consensus docking method for prediction of protein-ligand interactions

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

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

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SeleX-CS: A New Consensus Scoring Algorithm for Hit Discovery and Lead Optimization

(2009) Shay Bar-Haim et al.   Journal of Chemical Information and Modeling

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Prediction of the Water Content in Protein Binding Sites

(2009) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A genetic algorithm optimized fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease

(2008) Levente Fabry-Asztalos et al.   BIOORGANIC & MEDICINAL CHEMISTRY

SFCscore: Scoring functions for affinity prediction of protein-ligand complexes

(2008) Christoph A. Sotriffer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY