ArticlePloS one2014
Non-redundant unique interface structures as templates for modeling protein interactions.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function.Journal of molecular biology · 2025Review
- DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation.Bioinformatics (Oxford, England) · 2024Article
- ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations.Journal of chemical information and modeling · 2024Article
- Conformational diversity and protein-protein interfaces in drug repurposing in Ras signaling pathway.Scientific reports · 2024Article
- DeepBindPPI: Protein-Protein Binding Site Prediction Using Attention Based Graph Convolutional Network.The protein journal · 2023Article
- Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions.Frontiers in oncology · 2023Review
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- mPPI: a database extension to visualize structural interactome in a one-to-many manner.Database : the journal of biological databases and curation · 2021Article
- Assessment of protein-protein interfaces in cryo-EM derived assemblies.Nature communications · 2021Article
- Structural motifs in protein cores and at protein-protein interfaces are different.Protein science : a publication of the Protein Society · 2021Article
- Mutation Edgotype Drives Fitness Effect in Human.Frontiers in bioinformatics · 2021Article
- Advances in integrative structural biology: Towards understanding protein complexes in their cellular context.Computational and structural biotechnology journal · 2021Review
- A Review of Deep Learning Methods for Antibodies.Antibodies (Basel, Switzerland) · 2020Review
- Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Oncoviruses Can Drive Cancer by Rewiring Signaling Pathways Through Interface Mimicry.Frontiers in oncology · 2019Article
- Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Efficient flexible backbone protein-protein docking for challenging targets.Bioinformatics (Oxford, England) · 2018Article
- A Novel Geometry-Based Approach to Infer Protein Interface Similarity.Scientific reports · 2018Article
- Protein-protein interaction specificity is captured by contact preferences and interface composition.Bioinformatics (Oxford, England) · 2018Article
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions. Classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are 22604 unique interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at http://prism.ccbb.ku.edu.tr/piface.
Indexed as
Identifiers
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.