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E-raamat: Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Edited by (Central South University, China), Edited by (Central South University, China), Series edited by (University of Western Australia), Edited by (Georgia State University)
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Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics

This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems.

Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics:





Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures

Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.
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(38)
Anamika Basu
Anasua Sarkar
2 Protein Sequence Motif Information Discovery
41(16)
Bernard Chen
3 Identifying Calcium Binding Sites In Proteins
57(14)
Hui Liu
Hai Deng
4 Review Of Imbalanced Data Learning For Protein Methylation Prediction
71(20)
Zejin Ding
Yan-Qing Zhang
5 Analysis And Prediction Of Protein Posttranslational Modification Sites
91(18)
Jianjiong Gao
Qiuming Yao
Curtis Harrison Bollinger
Dong Xu
II Protein Analysis And Prediction
6 Protein Local Structure Prediction
109(16)
Wei Zhong
Jieyue He
Robert W. Harrison
Phang C. Tai
Yi Pan
7 Protein Structural Boundary Prediction
125(28)
Gulsah Altun
8 Prediction Of RNA Binding Sites In Proteins
153(18)
Zhi-Ping Liu
Luonan Chen
9 Algorithmic Frameworks For Protein Disulfide Connectivity Determination
171(34)
Rahul Singh
William Murad
Timothy Lee
10 Protein Contact Order Prediction: Update
205(12)
Yi Shi
Jianjun Zhou
David S. Wishart
Guohui Lin
11 Progress In Prediction Of Oxidation States Of Cysteines Via Computational Approaches
217(14)
Aiguo Du
Hui Liu
Hai Deng
Yi Pan
12 Computational Methods In Cryoelectron Microscopy 3D Structure Reconstruction
231(24)
Fa Zhang
Xiaohua Wan
Zhiyong Liu
III Protein Structure Alignment And Assessment
13 Fundamentals Of Protein Structure Alignment
255(26)
Mark Brandt
Allen Holder
Yosi Shibberu
14 Discovering 3D Protein Structures For Optimal Structure Alignment
281(18)
Tomas Novosad
Vaclav Snasel
Ajith Abraham
Jack Y. Yang
15 Algorithmic Methodologies For Discovery Of Nonsequential Protein Structure Similarities
299(18)
Bhaskar DasGupta
Joseph Dundas
Jie Liang
16 Fractal Related Methods For Predicting Protein Structure Classes And Functions
317(22)
Zu-Guo Yu
Vo Anh
Jian-Yi Yang
Shao-Ming Zhu
17 Protein Tertiary Model Assessment
339(18)
Anjum Chida
Robert W. Harrison
Yan-Qing Zhang
IV Protein-Protein Analysis Of Biological Networks
18 Network Algorithms For Protein Interactions
357(20)
Suely Oliveira
19 Identifying Protein Complexes From Protein-Protein Interaction Networks
377(16)
Jianxin Wang
Min Li
Xiaoqing Peng
20 Protein Functional Module Analysis With Protein--Protein Interaction (PPI) Networks
393(20)
Lei Shi
Xiujuan Lei
Aidong Zhang
21 Efficient Alignments Of Metabolic Networks With Bounded Treewidth
413(18)
Qiong Cheng
Piotr Berman
Robert W. Harrison
Alexander Zelikovsky
22 Protein-Protein Interaction Network Alignment: Algorithms And Tools
431(20)
Valeria Fionda
V Application Of Protein Bioinformatics
23 Protein-Related Drug Activity Comparison Using Support Vector Machines
451(10)
Wei Zhong
Jieyue He
24 Finding Repetitions In Biological Networks: Challenges, Trends, And Applications
461(20)
Simona E. Rombo
25 Me TaDoR: Online Resource And Prediction Server For Membrane Targeting Peripheral Proteins
481(14)
Nitin Bhardwaj
Morten Kallberg
Wonhwa Cho
Hui Liu
26 Biological Networks--Based Analysis Of Gene Expression Signatures
495(12)
Gang Chen
Jianxin Wang
Index 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.