Often considered the workhorse of the cellular machinery, proteins are responsible for functions ranging from molecular motors to signaling. The broad recognition of their involvement in all cellular processes has led to focused efforts to predict their functions from sequences, and if available, from their structures. An overview of current research directions, Computational Protein-Protein Interactions examines topics in the prediction of protein-protein interactions, including interference with protein-protein interactions and their design.
Explores Computational Approaches to Understanding Protein-Protein Interactions
Outlining fundamental and applied aspects of the usefulness of computations when approaching protein-protein interactions, this book incorporates different views of the same biochemical problem from sequence to structure to energetics. It covers protein-protein interaction prediction and dynamics, design, drug design for inhibition, and uses for the prediction of function. The text provides general chapters that overview the topic and also includes advanced material. The chapters detail the complexity of protein interaction studies and discuss potential caveats.
Addresses the Next Big Problem in Molecular Biology
While it is important to predict protein associations, this is a daunting task. Edited by two experts in the field and containing contributions from those at the forefront of research, the book provides a basic outline of major directions in computational protein-protein interactions research at the heart of functional genomics and crucial for drug discovery. It addresses the next big problem in molecular biology: how to create links between all the pieces of the cell jigsaw puzzle.
Table of Contents
Basic Principles of Protein–Protein Interaction, J. Janin
Low-Resolution Recognition Factors Determine Major Characteristics of the Energy Landscape in Protein–Protein Interaction, I.A. Vakser
The Molecular Architecture of Protein–Protein Binding Sites, E.J. Sundberg
Mapping Protein Function by Combinatorial Mutagenesis, G. Pál and S.S. Sidhu
The Association of Protein–Protein Complexes, G. Schreiber
Computational Simulations of Protein–Protein and Protein–Nucleic Acid Association, G.V. Pachov, R.R. Gabdoulline, and R.C. Wade
Computational Design of Protein–Protein Interactions, J.M. Shifman
Protein–Protein Docking, H. Hwang, B. Pierce, and Z. Weng
Prediction of Protein Interaction Sites, Y. Ofran
Predicting Molecular Interactions in Structural Proteomics, I. Kufareva and R. Abagyan
Rearrangements and Expansion of the Domain Content in Proteins Frequently Increase the Protein Connectivity in the Protein–Protein Interaction Network, I. Cohen-Gihon, R. Sharan, and R. Nussinov
Intrinsically Disordered Proteins and Their Recognition Functions, V.N. Uversky, M. Fuxreiter, C.J. Oldfield, A.K. Dunker, and P. Tompa
Identification of Druggable Hot Spots on Proteins and in Protein–Protein Interfaces, D. Beglov, R. Brenke, G.-Y. Chuang, D. Hall, M. Landon, C.H. Ngan, Y. Shen, S. Thiel, B. Zerbe, D. Kozakov, and S. Vajda
Designing Protein–Protein Interaction Inhibitors, M. Montes