Back to Browse Journals » Advances and Applications in Bioinformatics and Chemistry » Volume 2

Computer applications for prediction of protein–protein interactions and rational drug design

Authors Solène Grosdidier, Max Totrov, Juan Fernández-Recio

Published 10 November 2009 Volume 2009:2 Pages 101—123


Review by Single-blind

Peer reviewer comments 3

Solène Grosdidier1, Max Totrov2, Juan Fernández-Recio1

1Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain; 2Molsoft LLC, La Jolla, CA, USA

Abstract: In recent years, protein–protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein–protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Among them, computational docking aims to predict the structure of a protein–protein complex starting from the atomic coordinates of its individual components, and in recent years, a growing number of docking approaches are being reported with increased predictive capabilities. The improvement of speed and accuracy of these docking methods, together with the modeling of the interaction networks that regulate the most critical processes in a living organism, will be essential for computational proteomics. The ultimate goal is the rational design of drugs capable of specifically inhibiting or modifying protein–protein interactions of therapeutic significance. While rational design of protein–protein interaction inhibitors is at its very early stage, the first results are promising.

Keywords: protein–protein interactions, drug design, protein docking, structural prediction, virtual ligand screening, hot-spots

Download Article [PDF] 

Creative Commons License This work is published by Dove Medical Press Limited, and licensed under Creative Commons Attribution - Non Commercial (unported, v3.0) License. The full terms of the License are available at Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. Permissions beyond the scope of the License are administered by Dove Medical Press Limited. Information on how to request permission may be found at:

Other article by this author:

Refinement of rigid-body protein–protein docking using backbone and side-chain minimization with a coarse-grained model

Albert Solernou, Juan Fernández-Recio

Open Access Bioinformatics 2010, 2:19-27

Published Date: 13 April 2010

Readers of this article also read:

Development and optimization of a self-microemulsifying drug delivery system for atorvastatin calcium by using D-optimal mixture design

Yeom DW, Song YS, Kim SR, Lee SG, Kang MH, Lee S, Choi YW

International Journal of Nanomedicine 2015, 10:3865-3878

Published Date: 5 June 2015

Communicating sexual health messages: young adults and the female condom

Markham Shaw C, Chatterjee K

Open Access Journal of Contraception 2014, 5:29-37

Published Date: 30 June 2014

Bosutinib in the management of chronic myelogenous leukemia

Keller-von Amsberg G, Schafhausen P

Biologics: Targets and Therapy 2013, 7:115-122

Published Date: 6 May 2013

Patient acceptability of the Tecnis® multifocal intraocular lens

Sood P, Woodward MA

Clinical Ophthalmology 2011, 5:403-410

Published Date: 24 March 2011

MODENA: a multi-objective RNA inverse folding

Akito Taneda

Advances and Applications in Bioinformatics and Chemistry 2011, 4:1-12

Published Date: 22 December 2010

Occupational safety among dental health-care workers

Shigehiro Shimoji, Kohji Ishihama, Hidefumi Yamada, et al

Advances in Medical Education and Practice 2010, 1:41-47

Published Date: 11 October 2010

The effects of heterogeneity on Simon Phase II clinical trial design operating characteristics

Christopher N Barnes, Shesh N Rai

Open Access Journal of Clinical Trials 2010, 2:107-114

Published Date: 5 July 2010