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. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.
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1 Introduction to Structural Bioinformatics |
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1 | (10) |
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| Part I Advances in Methods for Structural Bioinformatics |
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2 JVM: Java Visual Mapping Tool for Next Generation Sequencing Read |
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11 | (8) |
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3 Advancement of Polarizable Force Field and Its Use for Molecular Modeling and Design |
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19 | (14) |
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4 Systematic Methods for Defining Coarse-Grained Maps in Large Biomolecules |
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33 | (16) |
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5 Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method |
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49 | (22) |
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6 Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems |
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71 | (14) |
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| Part II 3D-Structure Prediction and Folding Mechanism of Biological Macromolecules |
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7 Extended Structure of Rat Islet Amyloid Polypeptide in Solution |
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85 | (8) |
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Malathy Sony Subramanian Manimekalai |
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8 Folding Mechanisms of Trefoil Knot Proteins Studied by Molecular Dynamics Simulations and Go-model |
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93 | (18) |
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9 Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation |
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111 | (12) |
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10 Theoretical Studies on the Folding Mechanisms for Different DNA G-quadruplexes |
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123 | (20) |
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11 RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics |
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143 | (44) |
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| Part III The Interactions Between Biological Macromolecules and Ligands |
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12 Binding Modes and Interaction Mechanism Between Different Base Pairs and Methylene Blue Trihydrate: A Quantum Mechanics Study |
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187 | (18) |
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13 Drug Inhibition and Proton Conduction Mechanisms of the Influenza A M2 Proton Channel |
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205 | (22) |
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14 Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods and Applications |
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227 | (34) |
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| Part IV Functional Analysis of Biological Macromolecules |
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15 Evolutionary Optimization of Transcription Factor Binding Motif Detection |
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261 | (14) |
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16 Prediction of Serine/Threonine Phosphorylation Sites in Bacteria Proteins |
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275 | (12) |
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17 Bioinformatics Tools for Discovery and Functional Analysis of Single Nucleotide Polymorphisms |
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287 | (24) |
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18 An Application of QM/MM Simulation: The Second Protonation of Cytochrome P450 |
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311 | (16) |
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| Part V Application of Structural Bioinformatics in Drug Design |
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19 Recent Progress on Structural Bioinformatics Research of Cytochrome P450 and Its Impact on Drug Discovery |
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327 | (14) |
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20 Human Cytochrome P450 and Personalized Medicine |
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341 | (12) |
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21 The α7 nAChR Selective Agonists as Drug Candidates for Alzheimer's Disease |
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353 | (14) |
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22 Bayesian Analysis of Complex Interacting Mutations in HIV Drug Resistance and Cross-Resistance |
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Dr. Dongqing Wei is professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, China. He serves as Editor-in-Chief for journal of Interdisciplinary Sciences-Computational Life Sciences. He is chairman of International Association of Scientists in the Interdisciplinary Areas (IASIA). Prof. Weis research is in the general area of structural bioinformatics. He has made many important contributions to sciences. With more than 150 journal papers and SCI 3000 citations, he is becoming a leading figure in the area of structural bioinformatics. Prof. Wei organized a few important international conferences recently, for example, International Conference on Computational and System Biology, 2009-2011, Shanghai, China; Theory and Application of Computational Chemistry, Sept. 23-27, 2008, Shanghai, China; 2nd IEEE Conferences on Bioinformatics and Biomedical Engineering, May 16-20, 2008, Shanghai, China.
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