ArticleBMC bioinformatics2025
A comprehensive survey of scoring functions for protein docking models.
Article in BMC bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Discovery of a novel and potent KRASJournal of enzyme inhibition and medicinal chemistry · 2026Article
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- Structural T-Cell Receptor Analysis in the Age of Machine Learning.Immunological reviews · 2026Review
- BiMba: using Vision Mamba to predict protein sites that bind other proteins.Bioinformatics (Oxford, England) · 2026Article
- Polymer-stabilized amorphous CuO-ZnO hybrid nanocomplex as a promising candidate for antimicrobial therapy and controlled drug delivery with molecular docking insights.Scientific reports · 2026Article
- ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoupling Size from Shape: Cellular Sheaf Laplacians as Ligand Geometry Descriptors for Binding Affinity Prediction.International journal of molecular sciences · 2026Article
- Chrysotoxine Attenuates Key Atherogenic Processes via Antioxidant, Anti-Inflammatory, and COX-Dependent Antiplatelet Mechanisms.Biomolecules · 2026Article
- Integrated Computer-Aided Drug Design: Advances in GPCR Natural Ligand Discovery.Cell biochemistry and biophysics · 2026Review
- Chemical Profiling, Molecular Docking, and Mechanistic Anticancer Activity ofMolecules (Basel, Switzerland) · 2026Article
- In silico evaluation of the anti Helicobacter pylori activity of selected bioactive compounds from Aloe vera.Scientific reports · 2025Article
- Accurate site-specific folding via conditional diffusion based on AlphaFold3.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Accurate Site-specific Folding via Conditional Diffusion Based on Alphafold3.bioRxiv : the preprint server for biology · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundWhile protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurate and efficient scoring functions to differentiate between native and non-native binding complexes, the accuracy of current docking tools cannot be guaranteed. Although many innovative scoring functions have been proposed, a good scoring function for docking remains elusive. Deep learning models offer alternatives to using explicit empirical or mathematical functions for scoring protein-protein complexes.
resultsIn this study, we perform a comprehensive survey of the state-of-the-art scoring functions by considering the most popular and highly performant approaches, both classical and deep learning-based, for scoring protein-protein complexes. The methods were also compared based on their runtime as it directly impacts their use in large-scale docking applications.
conclusionsWe evaluate the strengths and weaknesses of classical and deep learning-based approaches across seven public and popular datasets to aid researchers in understanding the progress made in this field.
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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.