Emphasizing the role of proteins in construction of the developmental genetic toolkit in plants / Anamika Basu and Anasua Sarkar -- Protein sequence motif information discovery / Bernard Chen -- Identifying calcium binding sites in proteins / Hui Liu and Hai Deng -- Review of imbalanced data learning for protein methylation prediction / Zejin Ding and Yan-Quin Zhang -- Analysis and prediction of protein posttranslational modification sites / Jianjiong Gao, Qiuming Yao, Curtis Harris Bollinger, and Dong Xu -- Protein local structure prediction / Wei Zhong, Jieyue He, Robert W. Harrison, Phang C. Tai, and Yi Pan -- Protein structural boundary prediction / Gulsah Altun -- Predictions of RNA binding sites in proteins / Zhi-Ping and Luonan Chen -- Algorithmic frameworks for protein disufide connectivity determination / Rahul Singh, William Murad, and Timothy Lee -- Protein contact order prediction: update / Yi Shi, Jianjun Zhou, David S. Wishart. and Guohui Lin -- Progess in prediction of oxidation states of cysteines via computational approaches / Aiguo Du, Hui Liu, Hai Deng, and Yi Pan -- Computational methods in cryoelectron microscopy 3D structure reconsctruction / Fa Zhang, Xiaohua Wan, and Zhiyong Liu -- Fundamentals of protein structure alignment / Mark Brandt, Allen Holder, And Yoshi Shibberu -- Discovering 3D protein structures for optimal structure alignment / Tomas Novosad, Vaclav Snasel, Ajith Abraham, and Jack Y. Yang -- Algorithmic methodologies for discovery of nonsequential protein structure similarities / Bhaskar DasGupta, Joseph Dundas, and Jie Liang -- Fractal related methods for predicting protein structure classes and functions / Zu-Guo, Vo Anh, Jian- Yi Yang, Shao-Ming Zhu -- Protein tertiary model assessment / Anjum Chida, Robert W. Harrison, and Yan-Quing Zhang -- Network algorithms for protein interactions / Suely Oliveira -- Identifying protein complexes from protein-protein interaction networks / Jianxin Wang, Min Li, and Xiaoqing Peng -- Protein functional module analysis with protein-protein interaction (PPI) networks / Lei Shi, Xiujuan Lei, and Aidong Zhang -- Efficient alignment of metabolic networks with bounded treedwidth / Qiong Cheng, Piotr Berman, Robert W. Harrison, and Alexander Zelikovsky -- Protein-protein interaction network alignment: algorithms and tools / Valeria Fionda -- Protein-related drug activity comparison using support vector machines / Wei Zhong and Jieyue He -- Finding repetitions in biological networks: challenges, trends, and applications / Simona E. Rombo -- MeTaDoR: online resource and prediction server for membrane targeting peripheral proteins / Nitin Bhardwaj, Morten Kallberg, Wonhwa Cho, and Hui Lu -- Biological Networks-based analysis of gene expression signature / Gang Chen and Jianxin Wang.

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