ArticleNature protocols2011
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
What it found
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Who cites it
144 citing papers in PubMed.
- A robust framework for protein-protein interaction prediction with multi-objective ensemble learning and embedding-based representations.Scientific reports · 2026Article
- Hotspot Interactions between Two Fab Molecules in Molecular Dynamics Simulations Improve Predictive Models of Aggregation Kinetics.Molecular pharmaceutics · 2026Article
- Age-dependent elevation of Nr4a1 attenuates PI3K/AKT/GSK3β pathway and mediates tau hyperphosphorylation and cognitive impairments.Journal of advanced research · 2026Article
- Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.Journal of molecular biology · 2025Review
- Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway.Scientific reports · 2024Article
- Assessment of Protein-Protein Docking Models Using Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands.Antioxidants (Basel, Switzerland) · 2023Article
- Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis.Interdisciplinary sciences, computational life sciences · 2023Article
- Structural coverage of the human interactome.Briefings in bioinformatics · 2023Article
- Monoclonal antibody designed for SARS-nCoV-2 spike protein of receptor binding domain on antigenic targeted epitopes for inhibition to prevent viral entry.Molecular diversity · 2023Article
- Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites.Methods in molecular biology (Clifton, N.J.) · 2023Article
- CC16 drives VLA-2-dependent SPLUNC1 expression.Frontiers in immunology · 2023Article
- The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans.Life science alliance · 2022Article
- Astrocytic NDRG2-PPM1A interaction exacerbates blood-brain barrier disruption after subarachnoid hemorrhage.Science advances · 2022Article
- Computer-Aided Drug Design Boosts RAS Inhibitor Discovery.Molecules (Basel, Switzerland) · 2022Review
- Molecular Modelling Hurdle in the Next-Generation Sequencing Era.International journal of molecular sciences · 2022Article
- Integrating protein copy numbers with interaction networks to quantify stoichiometry in clathrin-mediated endocytosis.Scientific reports · 2022Article
- Rationally targeted anti-VISTA antibody that blockades the C-C' loop region can reverse VISTA immune suppression and remodel the immune microenvironment to potently inhibit tumor growth in an Fc independent manner.Journal for immunotherapy of cancer · 2022Article
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention.Biomolecules · 2021Review
84 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) for large-scale prediction of protein-protein interactions and assembly of protein complex structures. The method consists of two components: rigid-body structural comparisons of target proteins to known template protein-protein interfaces and flexible refinement using a docking energy function. The PRISM rationale follows our observation that globally different protein structures can interact via similar architectural motifs. PRISM predicts binding residues by using structural similarity and evolutionary conservation of putative binding residue 'hot spots'. Ultimately, PRISM could help to construct cellular pathways and functional, proteome-scale annotation. PRISM is implemented in Python and runs in a UNIX environment. The program accepts Protein Data Bank-formatted protein structures and is available at http://prism.ccbb.ku.edu.tr/prism_protocol/.
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