ArticleJournal of computer-aided molecular design1997
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes.
Article in Journal of computer-aided molecular design, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 478 papers, 1 of them a synthesis that pooled it.
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Who cites it
478 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- RA-PLA: Retrieval-augmented graph convolutional networks for protein-ligand binding affinity prediction.PloS one · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- A geometric graph-based deep learning model for drug-target affinity prediction.BMC bioinformatics · 2025Article
- Evaluation of NTD-O2, a Ghanaian herbal medicine, for onchocerciasis and animal African trypanosomiasis.BMC complementary medicine and therapies · 2025Article
- Structure-based identification of a non-covalent thioredoxin reductase inhibitor with proven ADMET suitability.Journal of enzyme inhibition and medicinal chemistry · 2025Article
- Assessing the accuracy of binding pose prediction for kinase proteins and 7-azaindole inhibitors: a study with AutoDock4, Vina, DOCK 6, and GNINA 1.0.RSC advances · 2025Article
- Rapid, accurate, and reproduciblemSphere · 2025Article
- Rivastigmine Templates with Antioxidant Motifs-A Medicinal Chemist's Toolbox Towards New Multipotent AD Drugs.Antioxidants (Basel, Switzerland) · 2025Article
418 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This paper describes the development of a simple empirical scoring function designed to estimate the free energy of binding for a protein-ligand complex when the 3D structure of the complex is known or can be approximated. The function uses simple contact terms to estimate lipophilic and metal-ligand binding contributions, a simple explicit form for hydrogen bonds and a term which penalises flexibility. The coefficients of each term are obtained using a regression based on 82 ligand-receptor complexes for which the binding affinity is known. The function reproduces the binding affinity of the complexes with a cross-validated error of 8.68 kJ/mol. Tests on internal consistency indicate that the coefficients obtained are stable to changes in the composition of the training set. The function is also tested on two test sets containing a further 20 and 10 complexes, respectively. The deficiencies of this type of function are discussed and it is compared to approaches by other workers.
Indexed as
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.