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Ligand Identification Scoring Algorithm (LISA)

https://doi.org/10.1021/ci2000665

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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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199908)20:11<1165::aid-jcc7>3.0.co;2-aopenalex-snapshot

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

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Effect of ligand volume correction on PMF scoring

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Evaluation of a knowledge‐based potential of mean force for scoring docked protein–ligand complexes

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

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An all atom force field for simulations of proteins and nucleic acids

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YETI: An interactive molecular mechanics program for small‐molecule protein complexes

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

Automated docking with grid‐based energy evaluation

inferredcites →https://doi.org/10.1002/prot.10567openalex-snapshot

NH…O, OH…O, and CH…O hydrogen bonds in protein–ligand complexes: Strong and weak interactions in molecular recognition

inferredcites →https://doi.org/10.1002/prot.20512openalex-snapshot

Binding MOAD (Mother Of All Databases)

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

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

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SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex

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Let’s not forget tautomers

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The molecular surface package

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

inferredcites →https://doi.org/10.1016/j.str.2009.02.010openalex-snapshot

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

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/ci049733jopenalex-snapshot

An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci6004993openalex-snapshot

Supervised Consensus Scoring for Docking and Virtual Screening

inferredcites →https://doi.org/10.1021/ci800298zopenalex-snapshot

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

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

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

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A New Atom-Additive Method for Calculating Partition Coefficients

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Limits of Free Energy Computation for Protein−Ligand Interactions

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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A new force field for modeling metalloproteins

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Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides

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A new force field for molecular mechanical simulation of nucleic acids and proteins

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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/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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/jm8000373openalex-snapshot

Recent Developments in Fragment-Based Drug Discovery

inferredcites →https://doi.org/10.1021/jm8016464openalex-snapshot

Structural Artifacts in Protein−Ligand X-ray Structures: Implications for the Development of Docking Scoring Functions

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/jp0312518openalex-snapshot

Pairwise GB/SA Scoring Function for Structure-based Drug Design

inferredcites →https://doi.org/10.1021/jp807701hopenalex-snapshot

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

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:1011115820450openalex-snapshot

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

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/10.1093/nar/gkl999openalex-snapshot

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

inferredcites →https://doi.org/10.2174/156802609789207091openalex-snapshot

Docking Screens: Right for the Right Reasons?

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

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Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction

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Modeling of the phase equilibria of aqueous two-phase systems using three-dimensional neural network

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

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inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00697openalex-snapshot

EISA-Score: Element Interactive Surface Area Score for Protein–Ligand Binding Affinity Prediction

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00226openalex-snapshot

Rigidity Strengthening: A Mechanism for Protein–Ligand Binding

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AGL-Score: Algebraic Graph Learning Score for Protein–Ligand Binding Scoring, Ranking, Docking, and Screening

inferred← citeshttps://doi.org/10.1021/ci300493wopenalex-snapshot

ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions

inferred← citeshttps://doi.org/10.1021/ci300619xopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/ci5002026openalex-snapshot

Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2

inferred← citeshttps://doi.org/10.1021/ct4005992openalex-snapshot

The Movable Type Method Applied to Protein–Ligand Binding

inferred← citeshttps://doi.org/10.1038/s41570-018-0018-6openalex-snapshot

Metal–ligand interactions in drug design

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Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools

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The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins

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inferred← citeshttps://doi.org/10.1111/cbdd.12470openalex-snapshot

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