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 ixCONTRIBUTORS xvI FROM PROTEIN SEQUENCE TO STRUCTURE1 EMPHASIZING THE ROLE OF PROTEINS IN CONSTRUCTION OF THE DEVELOPMENTAL GENETIC TOOLKIT IN PLANTS 3Anamika Basu and Anasua Sarkar2 PROTEIN SEQUENCE MOTIF INFORMATION DISCOVERY 41Bernard Chen3 IDENTIFYING CALCIUM BINDING SITES IN PROTEINS 57Hui Liu and Hai Deng4 REVIEW OF IMBALANCED DATA LEARNING FOR PROTEIN METHYLATION PREDICTION 71Zejin Ding and Yan-Qing Zhang5 ANALYSIS AND PREDICTION OF PROTEIN POSTTRANSLATIONAL MODIFICATION SITES 91Jianjiong Gao, Qiuming Yao, Curtis Harrison Bollinger, and Dong XuII PROTEIN ANALYSIS AND PREDICTION6 PROTEIN LOCAL STRUCTURE PREDICTION 109Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and Yi Pan7 PROTEIN STRUCTURAL BOUNDARY PREDICTION 125Gulsah Altun8 PREDICTION OF RNA BINDING SITES IN PROTEINS 153Zhi-Ping Liu and Luonan Chen9 ALGORITHMIC FRAMEWORKS FOR PROTEIN DISULFIDE CONNECTIVITY DETERMINATION 171Rahul Singh, William Murad, and Timothy Lee10 PROTEIN CONTACT ORDER PREDICTION: UPDATE 205Yi Shi, Jianjun Zhou, David S. Wishart, and Guohui Lin11 PROGRESS IN PREDICTION OF OXIDATION STATES OF CYSTEINES VIA COMPUTATIONAL APPROACHES 217Aiguo Du, Hui Liu, Hai Deng, and Yi Pan12 COMPUTATIONAL METHODS IN CRYOELECTRON MICROSCOPY 3D STRUCTURE RECONSTRUCTION 231Fa Zhang, Xiaohua Wan, and Zhiyong LiuIII PROTEIN STRUCTURE ALIGNMENT AND ASSESSMENT13 FUNDAMENTALS OF PROTEIN STRUCTURE ALIGNMENT 255Mark Brandt, Allen Holder, and Yosi Shibberu14 DISCOVERING 3D PROTEIN STRUCTURES FOR OPTIMAL STRUCTURE ALIGNMENT 281Tomáš Novosád, Václav Snášel, Ajith Abraham, and Jack Y. Yang15 ALGORITHMIC METHODOLOGIES FOR DISCOVERY OF NONSEQUENTIAL PROTEIN STRUCTURE SIMILARITIES 299Bhaskar DasGupta, Joseph Dundas, and Jie Liang16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURE CLASSES AND FUNCTIONS 317Zu-Guo Yu, Vo Anh, Jian-Yi Yang, and Shao-Ming Zhu17 PROTEIN TERTIARY MODEL ASSESSMENT 339Anjum Chida, Robert W. Harrison, and Yan-Qing ZhangIV PROTEIN–PROTEIN ANALYSIS OF BIOLOGICAL NETWORKS18 NETWORK ALGORITHMS FOR PROTEIN INTERACTIONS 357Suely Oliveira19 IDENTIFYING PROTEIN COMPLEXES FROM PROTEIN–PROTEIN INTERACTION NETWORKS 377Jianxin Wang, Min Li, and Xiaoqing Peng20 PROTEIN FUNCTIONAL MODULE ANALYSIS WITH PROTEIN–PROTEIN INTERACTION (PPI) NETWORKS 393Lei Shi, Xiujuan Lei, and Aidong Zhang21 EFFICIENT ALIGNMENTS OF METABOLIC NETWORKS WITH BOUNDED TREEWIDTH 413Qiong Cheng, Piotr Berman, Robert W. Harrison, and Alexander Zelikovsky22 PROTEIN–PROTEIN INTERACTION NETWORK ALIGNMENT: ALGORITHMS AND TOOLS 431Valeria FiondaV APPLICATION OF PROTEIN BIOINFORMATICS23 PROTEIN-RELATED DRUG ACTIVITY COMPARISON USING SUPPORT VECTOR MACHINES 451Wei Zhong and Jieyue He24 FINDING REPETITIONS IN BIOLOGICAL NETWORKS: CHALLENGES, TRENDS, AND APPLICATIONS 461Simona E. Rombo25 MeTaDoR: ONLINE RESOURCE AND PREDICTION SERVER FOR MEMBRANE TARGETING PERIPHERAL PROTEINS 481Nitin Bhardwaj, Morten Källberg, Wonhwa Cho, and Hui Lu26 BIOLOGICAL NETWORKS–BASED ANALYSIS OF GENE EXPRESSION SIGNATURES 495Gang Chen and Jianxin WangINDEX 507

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 ixCONTRIBUTORS xvI FROM PROTEIN SEQUENCE TO STRUCTURE1 EMPHASIZING THE ROLE OF PROTEINS IN CONSTRUCTION OF THE DEVELOPMENTAL GENETIC TOOLKIT IN PLANTS 3Anamika Basu and Anasua Sarkar2 PROTEIN SEQUENCE MOTIF INFORMATION DISCOVERY 41Bernard Chen3 IDENTIFYING CALCIUM BINDING SITES IN PROTEINS 57Hui Liu and Hai Deng4 REVIEW OF IMBALANCED DATA LEARNING FOR PROTEIN METHYLATION PREDICTION 71Zejin Ding and Yan-Qing Zhang5 ANALYSIS AND PREDICTION OF PROTEIN POSTTRANSLATIONAL MODIFICATION SITES 91Jianjiong Gao, Qiuming Yao, Curtis Harrison Bollinger, and Dong XuII PROTEIN ANALYSIS AND PREDICTION6 PROTEIN LOCAL STRUCTURE PREDICTION 109Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and Yi Pan7 PROTEIN STRUCTURAL BOUNDARY PREDICTION 125Gulsah Altun8 PREDICTION OF RNA BINDING SITES IN PROTEINS 153Zhi-Ping Liu and Luonan Chen9 ALGORITHMIC FRAMEWORKS FOR PROTEIN DISULFIDE CONNECTIVITY DETERMINATION 171Rahul Singh, William Murad, and Timothy Lee10 PROTEIN CONTACT ORDER PREDICTION: UPDATE 205Yi Shi, Jianjun Zhou, David S. Wishart, and Guohui Lin11 PROGRESS IN PREDICTION OF OXIDATION STATES OF CYSTEINES VIA COMPUTATIONAL APPROACHES 217Aiguo Du, Hui Liu, Hai Deng, and Yi Pan12 COMPUTATIONAL METHODS IN CRYOELECTRON MICROSCOPY 3D STRUCTURE RECONSTRUCTION 231Fa Zhang, Xiaohua Wan, and Zhiyong LiuIII PROTEIN STRUCTURE ALIGNMENT AND ASSESSMENT13 FUNDAMENTALS OF PROTEIN STRUCTURE ALIGNMENT 255Mark Brandt, Allen Holder, and Yosi Shibberu14 DISCOVERING 3D PROTEIN STRUCTURES FOR OPTIMAL STRUCTURE ALIGNMENT 281Tomáš Novosád, Václav Snášel, Ajith Abraham, and Jack Y. Yang15 ALGORITHMIC METHODOLOGIES FOR DISCOVERY OF NONSEQUENTIAL PROTEIN STRUCTURE SIMILARITIES 299Bhaskar DasGupta, Joseph Dundas, and Jie Liang16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURE CLASSES AND FUNCTIONS 317Zu-Guo Yu, Vo Anh, Jian-Yi Yang, and Shao-Ming Zhu17 PROTEIN TERTIARY MODEL ASSESSMENT 339Anjum Chida, Robert W. Harrison, and Yan-Qing ZhangIV PROTEIN–PROTEIN ANALYSIS OF BIOLOGICAL NETWORKS18 NETWORK ALGORITHMS FOR PROTEIN INTERACTIONS 357Suely Oliveira19 IDENTIFYING PROTEIN COMPLEXES FROM PROTEIN–PROTEIN INTERACTION NETWORKS 377Jianxin Wang, Min Li, and Xiaoqing Peng20 PROTEIN FUNCTIONAL MODULE ANALYSIS WITH PROTEIN–PROTEIN INTERACTION (PPI) NETWORKS 393Lei Shi, Xiujuan Lei, and Aidong Zhang21 EFFICIENT ALIGNMENTS OF METABOLIC NETWORKS WITH BOUNDED TREEWIDTH 413Qiong Cheng, Piotr Berman, Robert W. Harrison, and Alexander Zelikovsky22 PROTEIN–PROTEIN INTERACTION NETWORK ALIGNMENT: ALGORITHMS AND TOOLS 431Valeria FiondaV APPLICATION OF PROTEIN BIOINFORMATICS23 PROTEIN-RELATED DRUG ACTIVITY COMPARISON USING SUPPORT VECTOR MACHINES 451Wei Zhong and Jieyue He24 FINDING REPETITIONS IN BIOLOGICAL NETWORKS: CHALLENGES, TRENDS, AND APPLICATIONS 461Simona E. Rombo25 MeTaDoR: ONLINE RESOURCE AND PREDICTION SERVER FOR MEMBRANE TARGETING PERIPHERAL PROTEINS 481Nitin Bhardwaj, Morten Källberg, Wonhwa Cho, and Hui Lu26 BIOLOGICAL NETWORKS–BASED ANALYSIS OF GENE EXPRESSION SIGNATURES 495Gang Chen and Jianxin WangINDEX 507