ReviewMolecules (Basel, Switzerland)2015
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.
Review in Molecules (Basel, Switzerland), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 25 citations in OpenAlex.
- Increasing the fraction of correct solutions in ensembles of protein-protein docking models by an iterative consensus algorithm.Protein science : a publication of the Protein Society · 2025Article
- In Silico Identification of Potential Antagonists Targeting the HPV16 E2-E1 Interaction: A Step Toward Novel Therapeutics for Cervical Cancer.Current issues in molecular biology · 2025Article
- Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.Bioinformatics advances · 2023Article
- Article
- Confrontation of AlphaFold models with experimental structures enlightens conformational dynamics supporting CYP102A1 functions.Scientific reports · 2022Article
- A random forest classifier for protein-protein docking models.Bioinformatics advances · 2022Article
- D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect.Molecules (Basel, Switzerland) · 2021Article
- The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses.BMC bioinformatics · 2020Article
- Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein-Protein Docking Poses.Frontiers in molecular biosciences · 2020Article
- Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.Molecules (Basel, Switzerland) · 2018Review
- Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models.PloS one · 2016Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.
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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.