ArticleNucleic acids research2023
PASSer: fast and accurate prediction of protein allosteric sites.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
31 citing papers in PubMed.
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- Protein-protein interaction-mediated signaling networks in ischemic stroke: from molecular mechanisms to therapeutic strategies.Acta pharmacologica Sinica · 2026Review
- A systematic evaluation of protein allosteric site prediction tools with independent datasets.Journal of computer-aided molecular design · 2026Article
- PRMT5 encourages cell migration and metastasis of tongue squamous cell carcinoma through methylating ΔNp63α.Cell death and differentiation · 2026Article
- The allosteric landscape of the Src kinase.Science advances · 2026Article
- Employing AlphaFold and TED to explore the structural impacts of stress-associated mutations in rice.Bioinformatics advances · 2026Article
- Discovery of Small Molecule Inhibitors against Polo-Like Kinase 1 Targeting Breast Cancer.Anti-cancer agents in medicinal chemistry · 2026Article
- A Twist of Fate: The Helix-Turn-Helix Motif inJournal of chemical information and modeling · 2025Article
- Dynamic Allostery: Evolution's Double-Edged Sword in Protein Function and Disease.Journal of molecular biology · 2025Review
- Prediction of enzyme function using an interpretable optimized ensemble learning framework.Chemical science · 2025Article
- Multi-Temperature Crystallography of S-Adenosylmethionine Decarboxylase Observes Dynamic Loop Motions.Biomolecules · 2025Article
- STINGAllo: a web server for high-throughput prediction of allosteric site-forming residues using internal protein nanoenvironment descriptors.Briefings in bioinformatics · 2025Article
- Article
- DeepAllo: allosteric site prediction using protein language model (pLM) with multitask learning.Bioinformatics (Oxford, England) · 2025Article
- AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools.ACS omega · 2025Article
- Fc-Binding Cyclopeptide Induces Allostery from Fc to Fab: Revealed Through in Silico Structural Analysis to Anti-Phenobarbital Antibody.Foods (Basel, Switzerland) · 2025Article
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors.Computational and structural biotechnology journal · 2024Article
- MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model.Journal of cheminformatics · 2024Article
- The value of protein allostery in rational anticancer drug design: an update.Expert opinion on drug discovery · 2024Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Allostery refers to the biological process by which an effector modulator binds to a protein at a site distant from the active site, known as allosteric site. Identifying allosteric sites is essential for discovering allosteric process and is considered a critical factor in allosteric drug development. To facilitate related research, we developed PASSer (Protein Allosteric Sites Server) at https://passer.smu.edu, a web application for fast and accurate allosteric site prediction and visualization. The website hosts three trained and published machine learning models: (i) an ensemble learning model with extreme gradient boosting and graph convolutional neural network, (ii) an automated machine learning model with AutoGluon and (iii) a learning-to-rank model with LambdaMART. PASSer accepts protein entries directly from the Protein Data Bank (PDB) or user-uploaded PDB files, and can conduct predictions within seconds. The results are presented in an interactive window that displays protein and pockets' structures, as well as a table that summarizes predictions of the top three pockets with the highest probabilities/scores. To date, PASSer has been visited over 49 000 times in over 70 countries and has executed over 6 200 jobs.
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What OpenQuestion holds
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.