ArticleJournal of molecular modeling2004
Structure-based method for analyzing protein-protein interfaces.
Article in Journal of molecular modeling, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- In Silico Approach for the Evaluation of the Potential Antiviral Activity of Extra Virgin Olive Oil (EVOO) Bioactive Constituents Oleuropein and Oleocanthal on Spike Therapeutic Drug Target of SARS-CoV-2.Molecules (Basel, Switzerland) · 2022Article
- Densest subgraph-based methods for protein-protein interaction hot spot prediction.BMC bioinformatics · 2022Article
- Potential activity of Linezolid against SARS-CoV-2 using electronic and molecular docking study.Journal of molecular modeling · 2021Article
- Predicting Hot Spot Residues at Protein-DNA Binding Interfaces Based on Sequence Information.Interdisciplinary sciences, computational life sciences · 2021Article
- Review
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Methods for Discovering and Targeting Druggable Protein-Protein Interfaces and Their Application to Repurposing.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Protein-protein interface hot spots prediction based on a hybrid feature selection strategy.BMC bioinformatics · 2018Article
- Structural insights into the Middle East respiratory syndrome coronavirus 4a protein and its dsRNA binding mechanism.Scientific reports · 2017Article
- Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System.International journal of molecular sciences · 2017Article
- Identifying Loop-Mediated Protein-Protein Interactions Using LoopFinder.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.Journal of medicinal chemistry · 2015Article
- Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.Biophysical journal · 2015Article
- Discrete structural features among interface residue-level classes.BMC bioinformatics · 2015Article
- ECMIS: computational approach for the identification of hotspots at protein-protein interfaces.BMC bioinformatics · 2014Article
- Non-redundant unique interface structures as templates for modeling protein interactions.PloS one · 2014Article
- Effect of mutation at the interface of Trp-repressor dimeric protein: a steered molecular dynamics simulation.European biophysics journal : EBJ · 2013Article
- Computational prediction of protein hot spot residues.Current pharmaceutical design · 2012Review
- From laptop to benchtop to bedside: structure-based drug design on protein targets.Current pharmaceutical design · 2012Review
- Rigorous assessment and integration of the sequence and structure based features to predict hot spots.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydrogen bond, hydrophobic and vdW interactions are the three major non-covalent interactions at protein-protein interfaces. We have developed a method that uses only these properties to describe interactions between proteins, which can qualitatively estimate the individual contribution of each interfacial residue to the binding and gives the results in a graphic display way. This method has been applied to analyze alanine mutation data at protein-protein interfaces. A dataset containing 13 protein-protein complexes with 250 alanine mutations of interfacial residues has been tested. For the 75 hot-spot residues (deltadelta G > or = 1.5 kcal mol(-1)), 66 can be predicted correctly with a success rate of 88%. In order to test the tolerance of this method to conformational changes upon binding, we utilize a set of 26 complexes with one or both of their components available in the unbound form. The difference of key residues exported by the program is 11% between the results using complexed proteins and those from unbound ones. As this method gives the characteristics of the binding partner for a particular protein, in-depth studies on protein-protein recognition can be carried out. Furthermore, this method can be used to compare the difference between protein-protein interactions and look for correlated mutation.
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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.