'
'Contents
Preface IX
Part 1 Computational Approaches 1 Chapter 1 Computational Methods for Prediction
of Protein-Protein Interaction Sites 3 Aleksey Porollo and Jaroslaw Meller Chapter 2 Advances in HumanProtein Interaction
-Interactive and lmmersive Molecular Simulations 27 Nicolas Ferey, Alex Tek, Benoist Laurent, Marc Piuzzi,
Zhihan Lu, Marc Baaden, Olivier Delalande, Matthieu Chavent, Christine Martin, Lorenzo Piccinali, Brian Katz,
Patrick Bourdot and Ludovic Autin Chapter 3 Protein lnteractome and Its
Application to Protein Function Prediction 65 Woojin Jung, Hyun-Hwan Jeong, and KiYoung Lee Chapter 4 Integrative Approach for Detection
of Functional Modules from
Protein-Protein Interaction Networks 97 Zelmina Lubovac-Pilav
Chapter 5 Mining Protein
Interaction Groups 113 Lusheng Wang
Chapter 6 Prediction of Combinatorial Protein-Protein Interaction from Expression Data Based on Conditional Probability 131 Takatoshi Fujiki, Etsuko Inoue,
Takuya Yoshihiro and Masaru Nakagawa Chapter 7 Inferring Protein-Protein Interactions (PPis)
Based on Computational Methods 147 Shuichi Hirose
VI Contents
Chapter 8 Slow Protein Conformational Change, Allostery and Network Dynamics 169
Fan Bai, Zhanghan Wu, Jianshi Jin, Phillip Hochendoner and Jianhua Xing
Chapter 9 Prediction of Protein Interaction Sites Using Mimotope Analysis 189
Jian Huang, Beibei Ru and Ping Dai
Chapter 10 Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence 207
J. Planas-lglesias, J. Bonet, M.A. Marfn-L6pez, E. Feliu, A. Gursoy and B. Oliva
Chapter 11 Computational Approaches to Predict Protein Interaction 231
Darby Tien-Hao Chang
Chapter 12 G-Protein Coupled Receptors:
Experimental and Computational Approaches 247
Amirhossein Sakhteman, Hamid Nadri and Alireza Moradi
Chapter 13 Computational Approaches to Elucidating Transient Protein-Protein Interactions, Predicting Receptor-ligand Pairings 259
Ernesto lacucci, Samuel Xavier de Souza and Yves Moreau
Chapter 14 Finding Protein Complexes via
Fuzzy Learning Vector Quantization Algorithm 273
Hamid Ravaee, Ali Masoudi-Nejad and Ali Moeini
Part 2 Experimental Approaches 285
Chapter 15 In Vivo Imaging of Protein-Protein Interactions 287
Hao Hong, Shreya Goel and Weibo Cai
Chapter 16 NMR Investigations on Ruggedness of Native State Energy Landscape in Folded Proteins 305
Poluri Maruthi Krishna Mohan
Chapter 17 Conformational and Disorder to Order Transitions in Proteins:
Structure I Function Correlation in Apolipoproteins 331
Jose Campos-Teran, Paola Mendoza-Espinosa, Rolando Castillo and Jaime Mas-Oiiva
Chapter 18 Protein-Protein Interactions in Salt Solutions 359
Part 3 Others
Chapter 19 Computational Tools and Databases for the Study
and Characterization of Protein Interactions 379 Jose Ramon Bias, Joan Segura and Narcis Fernandez-Fuentes Chapter 20 Protein-Protein Interaction Networks: Structures,
Evolution, and Application to Drug Design 405 Takeshi Hase and Yoshihito Niimura
Chapter 21 A Survey on Evolutionary Analysis in PPI Networks 427 Pavol Jancura and Elena Marchiori
Chapter 22 Scalable, Integrative Analysis
and Visualization of Protein Interactions 457 David Otasek, Chiara Pastrello and Igor Jurisica
