Keyword

binding affinity prediction

Description: The computational estimation of how strongly a ligand or other molecule binds to a target, often for molecular screening or drug design.

Primary topic: Computational Drug Discovery Methods (67%)

OpenAlex ID: keywords/binding-affinity-prediction

Improved protein–ligand docking using GOLD

2003 · Marcel L. Verdonk, Jason C. Cole, et al. · Proteins Structure Function and Bioinformatics · 3,070

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

2010 · Daniel Seeliger, Bert L. de Groot · Journal of Computer-Aided Molecular Design · 2,634

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

1997 · Matthew D. Eldridge, Christopher W. Murray, et al. · Journal of Computer-Aided Molecular Design · 1,687

Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm

2003 · Guosheng Wu, Daniel H. Robertson, et al. · Journal of Computational Chemistry · 1,566

The Many Roles of Computation in Drug Discovery

2004 · William L. Jorgensen · Science · 1,559

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, Yujie Wu, et al. · Journal of the American Chemical Society · 1,299

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

2002 · Renxiao Wang, Luhua Lai, et al. · Journal of Computer-Aided Molecular Design · 1,193

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A new method for predicting binding affinity in computer-aided drug design

1994 · Johan Åqvist, Carmen Medina, et al. · Protein Engineering Design and Selection · 1,185

Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations

2003 · Jeffrey J. Gray, Stewart Moughon, et al. · Journal of Molecular Biology · 1,127

Regulation of protein-ligand binding affinity by hydrogen bond pairing

2016 · Deliang Chen, Numan Oezguen, et al. · Science Advances · 932

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Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf

2003 · Holger Gohlke, David A. Case · Journal of Computational Chemistry · 860

Comparative Evaluation of 11 Scoring Functions for Molecular Docking

2003 · Renxiao Wang, Yipin Lu, et al. · Journal of Medicinal Chemistry · 848

Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors

2002 · Holger Gohlke, Gerhard Klebe · Angewandte Chemie International Edition · 844

Protein–Ligand Scoring with Convolutional Neural Networks

2017 · Matthew Ragoza, Joshua Hochuli, et al. · Journal of Chemical Information and Modeling · 829

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Binding Affinity via Docking: Fact and Fiction

2018 · Tatu Pantsar, Antti Poso · Molecules · 783

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Selection of DNA binding sites by regulatory proteins

1987 · Otto G. Berg, Peter H. von Hippel · Journal of Molecular Biology · 746

NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence

2007 · Morten Nielsen, Claus Lundegaard, et al. · PLoS ONE · 719

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Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

2025 · Saro Passaro, Gabriele Corso, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 689

PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching

2006 · Steven L. Dixon, Alexander M. Smondyrev, et al. · Chemical Biology & Drug Design · 676

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Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

2008 · Robert Abel, Tom Young, et al. · Journal of the American Chemical Society · 668

Virtual ligand screening: strategies, perspectives and limitations

2006 · Gerhard Klebe · Drug Discovery Today · 664

Contacts-based prediction of binding affinity in protein–protein complexes

2015 · Anna Vangone, Alexandre MJJ Bonvin · eLife · 663

Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

2009 · Zsolt Bikadi, Eszter Hazai · Journal of Cheminformatics · 659

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Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

2006 · Andrew R. Leach, Brian K. Shoichet, et al. · Journal of Medicinal Chemistry · 647

Advances and Challenges in Protein-Ligand Docking

2010 · Sheng-You Huang, Xiaoqin Zou · International Journal of Molecular Sciences · 643

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Works count: 5,050

Citation count: 127,200