Next Article in Journal
The Antioxidant Properties and Inhibitory Effects on HepG2 Cells of Chicory Cultivated Using Three Different Kinds of Fertilizers in the Absence and Presence of Pesticides
Next Article in Special Issue
Molecular Docking and Multivariate Analysis of Xanthones as Antimicrobial and Antiviral Agents
Previous Article in Journal
Synthesis of Novel 1-(4-Substituted pyridine-3-sulfonyl)-3-phenylureas with Potential Anticancer Activity
Previous Article in Special Issue
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
Article Menu

Export Article

Open AccessReview
Molecules 2015, 20(7), 12045-12060; doi:10.3390/molecules200712045

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

1
Department of Sciences and Technologies, University "Parthenope" of Naples, Centro Direzionale Isola C4, 80143 Naples, Italy
2
Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Saudi Arabia
*
Author to whom correspondence should be addressed.
Academic Editor: Rino Ragno
Received: 1 April 2015 / Revised: 8 June 2015 / Accepted: 17 June 2015 / Published: 1 July 2015
(This article belongs to the Special Issue Molecular Docking in Drug Design)
View Full-Text   |   Download PDF [2813 KB, uploaded 1 July 2015]   |  

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. View Full-Text
Keywords: ranking; scoring; analysis; docking decoys; docking models; consensus; contact maps; inter-molecular contacts; protein-protein interactions; structure prediction; interface; COCOMAPS; CONSRANK; CAPRI ranking; scoring; analysis; docking decoys; docking models; consensus; contact maps; inter-molecular contacts; protein-protein interactions; structure prediction; interface; COCOMAPS; CONSRANK; CAPRI
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Oliva, R.; Chermak, E.; Cavallo, L. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps. Molecules 2015, 20, 12045-12060.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]

Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top