ISBN-10:
1118345789
ISBN-13:
9781118345788
Pub. Date:
11/11/2013
Publisher:
Wiley
Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics / Edition 1

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics / Edition 1

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Product Details

ISBN-13: 9781118345788
Publisher: Wiley
Publication date: 11/11/2013
Series: Wiley Series in Bioinformatics Series , #22
Pages: 536
Product dimensions: 6.00(w) x 9.30(h) x 1.20(d)

About the Author

YI PAN, PhD, is the Chair and Full Professor in theDepartment of Computer Science at Georgia State University, and aVisiting Chair Professor in the School of Information Science andEngineering at Central South University in Changsha, China.

MIN LI, PhD, is Associate Professor in the School ofInformation Science and Engineering and a postdoctoral associate inthe State Key Laboratory of Medical Genetics at Central SouthUniversity in Changsha, China.

JIANXIN WANG, PhD, is Associate Dean and Full Professorin the School of Information Science and Engineering at CentralSouth University in Changsha, China.

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Table of Contents

PREFACE ix

CONTRIBUTORS xv

I FROM PROTEIN SEQUENCE TO STRUCTURE

1 EMPHASIZING THE ROLE OF PROTEINS IN CONSTRUCTION OF THEDEVELOPMENTAL 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 METHYLATIONPREDICTION 71
Zejin Ding and Yan-Qing Zhang

5 ANALYSIS AND PREDICTION OF PROTEIN POSTTRANSLATIONALMODIFICATION SITES 91
Jianjiong Gao, Qiuming Yao, Curtis Harrison Bollinger, and DongXu

II PROTEIN ANALYSIS AND PREDICTION

6 PROTEIN LOCAL STRUCTURE PREDICTION 109
Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and YiPan

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 CONNECTIVITYDETERMINATION 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 VIACOMPUTATIONAL APPROACHES 217
Aiguo Du, Hui Liu, Hai Deng, and Yi Pan

12 COMPUTATIONAL METHODS IN CRYOELECTRON MICROSCOPY 3D STRUCTURERECONSTRUCTION 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 STRUCTUREALIGNMENT 281
Tomáš Novosád, Václav Snášel,Ajith Abraham, and Jack Y. Yang

15 ALGORITHMIC METHODOLOGIES FOR DISCOVERY OF NONSEQUENTIALPROTEIN STRUCTURE SIMILARITIES 299
Bhaskar DasGupta, Joseph Dundas, and Jie Liang

16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURECLASSES 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 BIOLOGICALNETWORKS

18 NETWORK ALGORITHMS FOR PROTEIN INTERACTIONS 357
Suely Oliveira

19 IDENTIFYING PROTEIN COMPLEXES FROM PROTEIN–PROTEININTERACTION NETWORKS 377
Jianxin Wang, Min Li, and Xiaoqing Peng

20 PROTEIN FUNCTIONAL MODULE ANALYSIS WITH PROTEIN–PROTEININTERACTION (PPI) NETWORKS 393
Lei Shi, Xiujuan Lei, and Aidong Zhang

21 EFFICIENT ALIGNMENTS OF METABOLIC NETWORKS WITH BOUNDEDTREEWIDTH 413
Qiong Cheng, Piotr Berman, Robert W. Harrison, and AlexanderZelikovsky

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 VECTORMACHINES 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 MEMBRANETARGETING PERIPHERAL PROTEINS 481
Nitin Bhardwaj, Morten Källberg, Wonhwa Cho, and HuiLu

26 BIOLOGICAL NETWORKS–BASED ANALYSIS OF GENE EXPRESSIONSIGNATURES 495
Gang Chen and Jianxin Wang

INDEX 507

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