Introduction to structural bioinformatics / Qin Xu, Hao Dai, Tangzhen Zhao and Dongqing Wei -- Part I: Advances in methods for structural bioinformatics. JVM: java visual mapping tool for next generation sequencing read / Ye Yang and Juan Liu -- Advancement of polarizable force field and its use for molecular modeling and design / Xu, Peijun [and ten others] -- Systematic methods for defining coarse-grained maps in large biomolecules / Zhiyong Zhang -- Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method / Tong Zhu, John Z.H. Zhang and Xiao He -- Applications of rare event dynamics on the free energy calculations for membrane protein systems / Yukun Wang, Ruoxu Gu, Huaimeng Fan, Jakob Ulmschneider and Dongqing Wei -- Part II: 3-D structure prediction and folding mechanism of biological macromolecules. Extended structure of rat islet amyloid polypeptide in solution / Lei Wei [and six others] -- Folding mechanisms of trefoil knot proteins studied by molecular dynamics simulations and go-model / Xue Wu [and ten others] -- Binding induced intrinsically disordered protein folding with molecular dynamics simulation / Haifeng Chen -- Theoretical studies on the folding mechanisms for different DNA G-quadruplexes / Xue Wu [and ten others] -- RNA folding: structure prediction, folding kinetics and ion electrostatics / Zhijie Tan, Wenbing Zhang, Yazhou Shi and Fenghua Wang -- Part III: The interactions between biological macromolecules and ligands. Binding modes and interaction mechanism between different base pairs and methylene blue trihydrate: a quantum mechanics study / Peijun Xu [and eight others] -- Drug inhibition and proton conduction mechanisms of the influenza A M2 proton channel / Ruoxu Gu, Limin Angela Liu and Dongqing Wei -- Exploring the ligand-protein networks in traditional chinese medicine: current databases, methods and applications / Mingzhu Zhao and Dongqing Wei -- Part IV: Functional analysis of biological macromolecules. Evolutionary optimization of transcription factor binding motif detection / Zhao Zhang, Ze Wang, Guoqin Mai, Youxi Luo, Miaomiao Zhao and Fengfeng Zhou -- Prediction of serine/threonine phosphorylation sites in bacteria proteins / Zhengpeng Li, Ping Wu, Yuanyuan Zhao, Zexian Liu and Wei Zhao -- Bioinformatics tools for discovery and functional analysis of single nucleotide polymorphisms / Li Li and Dongqing Wei -- An application of QM/MM simulation: the second protonation of cytochrome P450 / Peng Lian and Dongqing Wei -- Part V: Application of structural bioinformatics in drug design. Recent progress on structural bioinformatics research of cytochrome P450 and its impact on drug discovery / Tao Zhang and Dongqing Wei -- Human cytochrome P450 and personalized medicine / Qi Chen and Dongqing Wei -- The [alpha]7 nAChR selective agonists as drug candidates for Alzheimer's disease / Huaimeng Fan, Ruoxu Gu and Dongqing Wei -- Bayesian analysis of complex interacting mutations in HIV drug resistance and cross-resistance / Ivan Kozyryev and Jing Zhang.
Summary:
"This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches."
Series:
Advances in experimental medicine and biology, 0065-2598 ; volume 827
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.