Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

YI PAN, PhD, is the Chair and Full Professor in the Department of Computer Science at Georgia State University, and a Visiting Chair Professor in the School of Information Science and Engineering at Central South University in Changsha, China. MIN LI, PhD, is Associate Professor in the School of Information Science and Engineering and a postdoctoral associate in the State Key Laboratory of Medical Genetics at Central South University in Changsha, China. JIANXIN WANG, PhD, is Associate Dean and Full Professor in the School of Information Science and Engineering at Central South University in Changsha, China.

PREFACE ix CONTRIBUTORS xv I FROM PROTEIN SEQUENCE TO STRUCTURE 1 EMPHASIZING THE ROLE OF PROTEINS IN CONSTRUCTION OF THE DEVELOPMENTAL GENETIC TOOLKIT IN PLANTS 3 Anamika Basu and Anasua Sarkar 2 PROTEIN SEQUENCE MOTIF INFORMATION DISCOVERY 41 Bernard Chen 3 IDENTIFYING CALCIUM BINDING SITES IN PROTEINS 57 Hui Liu and Hai Deng 4 REVIEW OF IMBALANCED DATA LEARNING FOR PROTEIN METHYLATION PREDICTION 71 Zejin Ding and Yan-Qing Zhang 5 ANALYSIS AND PREDICTION OF PROTEIN POSTTRANSLATIONAL MODIFICATION SITES 91 Jianjiong Gao, Qiuming Yao, Curtis Harrison Bollinger, and Dong Xu II PROTEIN ANALYSIS AND PREDICTION 6 PROTEIN LOCAL STRUCTURE PREDICTION 109 Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and Yi Pan 7 PROTEIN STRUCTURAL BOUNDARY PREDICTION 125 Gulsah Altun 8 PREDICTION OF RNA BINDING SITES IN PROTEINS 153 Zhi-Ping Liu and Luonan Chen 9 ALGORITHMIC FRAMEWORKS FOR PROTEIN DISULFIDE CONNECTIVITY DETERMINATION 171 Rahul Singh, William Murad, and Timothy Lee 10 PROTEIN CONTACT ORDER PREDICTION: UPDATE 205 Yi Shi, Jianjun Zhou, David S. Wishart, and Guohui Lin 11 PROGRESS IN PREDICTION OF OXIDATION STATES OF CYSTEINES VIA COMPUTATIONAL APPROACHES 217 Aiguo Du, Hui Liu, Hai Deng, and Yi Pan 12 COMPUTATIONAL METHODS IN CRYOELECTRON MICROSCOPY 3D STRUCTURE RECONSTRUCTION 231 Fa Zhang, Xiaohua Wan, and Zhiyong Liu III PROTEIN STRUCTURE ALIGNMENT AND ASSESSMENT 13 FUNDAMENTALS OF PROTEIN STRUCTURE ALIGNMENT 255 Mark Brandt, Allen Holder, and Yosi Shibberu 14 DISCOVERING 3D PROTEIN STRUCTURES FOR OPTIMAL STRUCTURE ALIGNMENT 281 Tomas Novosad, Vaclav Snasel, Ajith Abraham, and Jack Y. Yang 15 ALGORITHMIC METHODOLOGIES FOR DISCOVERY OF NONSEQUENTIAL PROTEIN STRUCTURE SIMILARITIES 299 Bhaskar DasGupta, Joseph Dundas, and Jie Liang 16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURE CLASSES AND FUNCTIONS 317 Zu-Guo Yu, Vo Anh, Jian-Yi Yang, and Shao-Ming Zhu 17 PROTEIN TERTIARY MODEL ASSESSMENT 339 Anjum Chida, Robert W. Harrison, and Yan-Qing Zhang IV PROTEIN--PROTEIN ANALYSIS OF BIOLOGICAL NETWORKS 18 NETWORK ALGORITHMS FOR PROTEIN INTERACTIONS 357 Suely Oliveira 19 IDENTIFYING PROTEIN COMPLEXES FROM PROTEIN--PROTEIN INTERACTION NETWORKS 377 Jianxin Wang, Min Li, and Xiaoqing Peng 20 PROTEIN FUNCTIONAL MODULE ANALYSIS WITH PROTEIN--PROTEIN INTERACTION (PPI) NETWORKS 393 Lei Shi, Xiujuan Lei, and Aidong Zhang 21 EFFICIENT ALIGNMENTS OF METABOLIC NETWORKS WITH BOUNDED TREEWIDTH 413 Qiong Cheng, Piotr Berman, Robert W. Harrison, and Alexander Zelikovsky 22 PROTEIN--PROTEIN INTERACTION NETWORK ALIGNMENT: ALGORITHMS AND TOOLS 431 Valeria Fionda V APPLICATION OF PROTEIN BIOINFORMATICS 23 PROTEIN-RELATED DRUG ACTIVITY COMPARISON USING SUPPORT VECTOR MACHINES 451 Wei Zhong and Jieyue He 24 FINDING REPETITIONS IN BIOLOGICAL NETWORKS: CHALLENGES, TRENDS, AND APPLICATIONS 461 Simona E. Rombo 25 MeTaDoR: ONLINE RESOURCE AND PREDICTION SERVER FOR MEMBRANE TARGETING PERIPHERAL PROTEINS 481 Nitin Bhardwaj, Morten Kallberg, Wonhwa Cho, and Hui Lu 26 BIOLOGICAL NETWORKS--BASED ANALYSIS OF GENE EXPRESSION SIGNATURES 495 Gang Chen and Jianxin Wang INDEX 507