Protein Interactions: Computational Methods, Analysis And Applications

The interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design. This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules. Contents: Protein–Protein Interactions: Structural and Dynamical Aspects of Evolutionarily Conserved Protein–Protein Complexes (Himani Tandon, Sneha Vishwanath and Narayanaswamy Srinivasan) A Comprehensive Overview of Sequence-Based Protein-Binding Residue Predictions for Structured and Disordered Regions (Amita Barik and Lukasz Kurgan) Prediction of Protein–Protein Complex Structures by Docking (Danial Pourjafar-Dehkordi and Martin Zacharias) Binding Affinity of Protein–Protein Complexes: Experimental Techniques, Databases and Computational Methods (M Michael Gromiha) Mutational Effects on Protein–Protein Interactions (Jackson Weako, Attila Gursoy and Ozlem Keskin) Predicting the Consequences of Mutations (Hemant Kumar and Julia M Shifman) Protein–Nucleic Acid Interactions: Computational Approaches for Understanding the Recognition Mechanism of Protein–Nucleic Acid Complexes (Ambuj Srivastava, Dhanusha Yesudhas, A Kulandaisamy, Nisha Muralidharan, C Ramakrishnan, R Nagarajan and M Michael Gromiha) Prediction of Nucleic Acid Binding Proteins and Their Binding Sites (Dhanusha Yesudhas, Ambuj Srivastava, Nisha Muralidharan, A Kulandaisamy, R Nagarajan and M Michael Gromiha) Predicting Protein–Binding Sites in Nucleic Acids (Kyungsook Han) Docking Algorithms and Scoring Functions (Arina Afanasyeva, Chioko Nagao and Kenji Mizuguchi) Recent Progress of Methodology Development for Protein–RNA Docking (Yun Guo, Xiaoyong Pan and Hong-Bin Shen) Protein–Ligand Interactions: Protein–Carbohydrate Complexes: Binding Site Analysis, Prediction, Binding Affinity and Molecular Dynamics Simulations (K Veluraja, N R Siva Shanmugam, J Jino Blessy, R A Jeyaram, B Lalithamaheswari and M Michael Gromiha) Quantitative Structure-Activity Relationship in Ligand-Based Drug Design: Concepts and Applications (Vishnupriya Kanakaveti, P Anoosha, R Sakthivel, S K Rayala and M Michael Gromiha) Protein–Ligand Interactions in Molecular Modeling and Structure-Based Drug Design (Devadasan Velmurugan, Dasararaju Gayathri, Chandrasekaran Ramakrishnan and Atanu Bhattacharjee) An Overview of Protein–Ligand Docking and Scoring Algorithms (Ruchika Bhat, Abhilash Jayaraj, Anjali Soni and B Jayaram) Readership: Graduate students and researchers working on protein interactions; researchers in the fields of bioinformatics, computational biology, computational chemistry, biochemistry, biophysics.Protein Interactions;Binding Sites;Prediction;Structural Analysis;Recognition Mechanism;Computational Methods;Protein-protein;Protein-RNA;Protein-DNA;Protein-ligand;Binding Affinity;Mutation;Databases;Web Servers;QSAR;Docking;Molecular Dynamics;Drug Design0 Key Features: Single unique source with concepts and applications on all types of protein complexesWritten by outstanding researchers in the field with easily understandable illustrationsCompilation of databases and online toolsUp-to-date literature and latest developments