ArticleJournal of molecular modeling2007
Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces.
Article in Journal of molecular modeling, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects.Genome biology · 2025Article
- Integrative modeling of guanylate binding protein dimers.Protein science : a publication of the Protein Society · 2023Article
- Differential Bias for Creatinine- and Cystatin C- Derived Estimated Glomerular Filtration Rate in Critical COVID-19.Biomedicines · 2022Article
- Roles of Physicochemical and Structural Properties of RNA-Binding Proteins in Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning.International journal of molecular sciences · 2022Article
- Article
- Protein-protein interaction specificity is captured by contact preferences and interface composition.Bioinformatics (Oxford, England) · 2018Article
- Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity.Bioinformatics (Oxford, England) · 2017Article
- Progress and challenges in predicting protein interfaces.Briefings in bioinformatics · 2016Review
- Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions.PLoS computational biology · 2015Article
- Predicting protein interface residues using easily accessible on-line resources.Briefings in bioinformatics · 2015Review
- Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions.Chemistry & biology · 2015Review
- AllerTOP v.2--a server for in silico prediction of allergens.Journal of molecular modeling · 2014Article
- Base of the measles virus fusion trimer head receives the signal that triggers membrane fusion.The Journal of biological chemistry · 2012Article
- Protein docking prediction using predicted protein-protein interface.BMC bioinformatics · 2012Article
- Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.PloS one · 2012Article
- Article
- Engineering cytochrome P450 biocatalysts for biotechnology, medicine and bioremediation.Expert opinion on drug metabolism & toxicology · 2010Review
- Structural analysis of linear and conformational epitopes of allergens.Regulatory toxicology and pharmacology : RTP · 2009Review
- Automated detection of conformational epitopes using phage display Peptide sequences.Bioinformatics and biology insights · 2009Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
We have developed a fully automated method, InterProSurf, to predict interacting amino acid residues on protein surfaces of monomeric 3D structures. Potential interacting residues are predicted based on solvent accessible surface areas, a new scale for interface propensities, and a cluster algorithm to locate surface exposed areas with high interface propensities. Previous studies have shown the importance of hydrophobic residues and specific charge distribution as characteristics for interfaces. Here we show differences in interface and surface regions of all physical chemical properties of residues as represented by five quantitative descriptors. In the current study a set of 72 protein complexes with known 3D structures were analyzed to obtain interface propensities of residues, and to find differences in the distribution of five quantitative descriptors for amino acid residues. We also investigated spatial pair correlations of solvent accessible residues in interface and surface areas, and compared log-odds ratios for interface and surface areas. A new scoring method to predict potential functional sites on the protein surface was developed and tested for a new dataset of 21 protein complexes, which were not included in the original training dataset. Empirically we found that the algorithm achieves a good balance in the accuracy of precision and sensitivity by selecting the top eight highest scoring clusters as interface regions. The performance of the method is illustrated for a dimeric ATPase of the hyperthermophile, Methanococcus jannaschii, and the capsid protein of Human Hepatitis B virus. An automated version of the method can be accessed from our web server at http://curie.utmb.edu/prosurf.html.
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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.