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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential

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BLEEP?potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data

inferredcites →https://doi.org/10.1002/1096-987x(200103)22:4<418::aid-jcc1012>3.0.co;2-3openalex-snapshot

Effect of ligand volume correction on PMF scoring

inferredcites →https://doi.org/10.1002/jcc.20505openalex-snapshot

An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function

inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot

Automated docking with grid‐based energy evaluation

inferredcites →https://doi.org/10.1002/prot.1087openalex-snapshot

A distance‐dependent atomic knowledge‐based potential for improved protein structure selection

inferredcites →https://doi.org/10.1006/jmbi.1996.0175openalex-snapshot

Statistical Potentials Extracted From Protein Structures: How Accurate Are They?

inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot

A Fast Flexible Docking Method using an Incremental Construction Algorithm

inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot

Knowledge-based scoring function to predict protein-ligand interactions

inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

inferredcites →https://doi.org/10.1007/s10822-012-9567-9openalex-snapshot

Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot

Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

inferredcites →https://doi.org/10.1016/s0022-2836(05)80068-3openalex-snapshot

Identification of native protein folds amongst a large number of incorrect models

inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot

Calculation of conformational ensembles from potentials of mena force

inferredcites →https://doi.org/10.1021/bk-1999-0719.ch019openalex-snapshot

Reduced Dimensionality in Ligand—Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial Libraries

inferredcites →https://doi.org/10.1021/ci2000665openalex-snapshot

Ligand Identification Scoring Algorithm (LISA)

inferredcites →https://doi.org/10.1021/ci200377uopenalex-snapshot

Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

inferredcites →https://doi.org/10.1021/ci9002987openalex-snapshot

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

inferredcites →https://doi.org/10.1021/ja960751uopenalex-snapshot

SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence

inferredcites →https://doi.org/10.1021/jm0105833openalex-snapshot

SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot

Comparative Evaluation of 11 Scoring Functions for Molecular Docking

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot

The PDBbind Database: Methodologies and Updates

inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot

A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes

inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot

DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction

inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot

A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

inferredcites →https://doi.org/10.1021/ma00145a039openalex-snapshot

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

inferredcites →https://doi.org/10.1023/a:1007999920146openalex-snapshot

Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs

inferredcites →https://doi.org/10.1023/a:1008729005958openalex-snapshot

A knowledge-based scoring function for protein-ligand interactions: Probing the reference state

inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

inferredcites →https://doi.org/10.1038/358086a0openalex-snapshot

A new approach to protein fold recognition

inferredcites →https://doi.org/10.1063/1.1749657openalex-snapshot

Statistical Mechanics of Fluid Mixtures

inferredcites →https://doi.org/10.1073/pnas.93.21.11628openalex-snapshot

An iterative method for extracting energy-like quantities from protein structures.

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Structure‐Based Drug Design

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Flexible CDOCKER : Development and application of a pseudo‐explicit structure‐based docking method within CHARMM

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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

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Refinement of pairwise potentials via logistic regression to score protein‐protein interactions

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RNA –ligand molecular docking: Advances and challenges

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Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery

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Feature functional theory–binding predictor (FFT–BP) for the blind prediction of binding free energies

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Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

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On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge

inferred← citeshttps://doi.org/10.1007/s10822-017-0068-8openalex-snapshot

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

inferred← citeshttps://doi.org/10.1007/s10822-018-0170-6openalex-snapshot

Overview of the SAMPL6 host–guest binding affinity prediction challenge

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Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method

inferred← citeshttps://doi.org/10.1007/s10822-021-00423-4openalex-snapshot

Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction

inferred← citeshttps://doi.org/10.1007/s12539-019-00327-wopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.008openalex-snapshot

Can docking scoring functions guarantee success in virtual screening?

inferred← citeshttps://doi.org/10.1016/j.bmc.2016.08.030openalex-snapshot

Incorporation of side chain flexibility into protein binding pockets using MTflex

inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108433openalex-snapshot

Binding and selectivity studies of phosphatidylinositol 3-kinase (PI3K) inhibitors

inferred← citeshttps://doi.org/10.1016/j.ymeth.2017.08.010openalex-snapshot

Function and structure-based screening of compounds, peptides and proteins to identify drug candidates

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00474openalex-snapshot

Development of a New Scoring Function for Virtual Screening: APBScore

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00334openalex-snapshot

DeepBSP—a Machine Learning Method for Accurate Prediction of Protein–Ligand Docking Structures

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00771openalex-snapshot

graphLambda: Fusion Graph Neural Networks for Binding Affinity Prediction

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00158openalex-snapshot

Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00339openalex-snapshot

Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot

Conformation Generation: The State of the Art

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00734openalex-snapshot

Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection

inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00356openalex-snapshot

Random Forest Refinement of Pairwise Potentials for Protein–Ligand Decoy Detection

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FFENCODER-PL: Pair Wise Energy Descriptors for Protein-Ligand Pose Selection

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Free Energy-Based Conformational Search Algorithm Using the Movable Type Sampling Method

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An Atomistic Statistically Effective Energy Function for Computational Protein Design

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Generation of Pairwise Potentials Using Multidimensional Data Mining

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Evaluation of Predicted Protein–Protein Complexes by Binding Free Energy Simulations

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Fast, Routine Free Energy of Binding Estimation Using MovableType

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Classification of Current Scoring Functions

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The Movable Type Method Applied to Protein–Ligand Binding

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KECSA-Movable Type Implicit Solvation Model (KMTISM)

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Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach

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Target identification among known drugs by deep learning from heterogeneous networks

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Computational analysis for residue-specific CDK2-inhibitor bindings

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GSScore: a novel Graphormer-based shell-like scoring method for protein–ligand docking

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Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model

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PDB-wide collection of binding data: current status of the PDBbind database

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ViTScore: A Novel Three-Dimensional Vision Transformer Method for Accurate Prediction of Protein–Ligand Docking Poses

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Freely Accessible Chemical Database Resources of Compounds for In Silico Drug Discovery

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Theoretical and computational modeling of rna-ligand interactions

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Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

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Molecular Modeling in Drug Design

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Molecular Modeling Studies on the Binding Mode of the PD-1/PD-L1 Complex Inhibitors

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