Structural bioinformatics / ed. by Gu J., Bourne P.E. - 2nd ed. - Hoboken: Wiley-Blackwell, 2009. - xxvi, 1035 p., [32] p. of plates: ill. (some col.). - Incl. bibl. ref. - Ind. - p.1019-1035. - ISBN 978-0-47018105-8  Место хранения:   06 | Якутский научный центр СО РАН | Якутск | Центральная научная библиотека Якутского научного центра СО РАН

Оглавление / Contents

Foreword ....................................................... xi Preface ........................................................ xv Acknowledgments ............................................... xix Contributors .................................................. xxi Section I DATA COLLECTION, ANALYSIS, AND VISUALIZATION ........ 1 1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS ........ 3 Russ B. Altman and Jonathan M. Dugan 2 FUNDAMENTALS OF PROTEIN STRUCTURE ........................... 15 Eric D. Scheeff and J. Lynn Fink 3 FUNDAMENTALS OF DNA AND RNA STRUCTURE ....................... 41 Stephen Neidle, Bohdan Schneider, and Helen M. Berman 4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION ...................... 77 Paul D. Adams, Ralf W. Grosse-Kunstleve, and Axel T. Brunger 5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY ................................................ 93 John L. Markley, Arash Bahrami, Hamid R. Eghbalnia, Francis C. Peterson, Robert C. Tyler, Eldon L. Ulrich, William M. Westler, and Brian F. Volkman 6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY .................................................... 143 Niels Volkmann and Dorit Hanein 7 STUDY OF PROTEIN THREE-DIMENSIONAL STRUCTURE AND DYNAMICS USING PEPTIDE AMIDE HYDROGEN/ DEUTERIUM EXCHANGE MASS SPECTROMETRY (DXMS) AND CHEMICAL CROSS-LINKING WITH MASS SPECTROMETRY TO CONSTRAIN MOLECULAR MODELING ............... 171 Sheng Li, Dmitri Mouradov, Gordon King, Tong Liu, Ian Ross, Bostjan Kobe, Virgil L. Woods Jr, and Thomas Huber 8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS ........... 207 Ian Samish 9 MOLECULAR VISUALIZATION .................................... 237 Steven Bottomley and Erik Helmerhorst Section II DATA REPRESENTATION AND DATABASES ................. 269 10 THE PDB FORMAT, mmCIF FORMATS, AND OTHER DATA FORMATS ...... 271 John D. Westbrook and Paula M.D. Fitzgerald 11 THE WORLDWIDE PROTEIN DATA BANK ............................ 293 Helen M. Berman, Kim Henrick, Haruki Nakamura, and John L. Markley 12 THE NUCLEIC ACID DATABASE .................................. 305 Bohdan Schneider, Joanna de la Cruz, Zukang Feng, Li Chen, Shuchismita Dutta, Irina Persikova, John D. Westbrook, Huanwang Yang, Jasmine Young, Christine Zardecki, and Helen M. Berman 13 OTHER STRUCTURE-BASED DATABASES ............................ 321 J. Lynn Fink, Helge Weissig, and Philip E. Bourne Section III DATA INTEGRITY AND COMPARATIVE FEATURES ........... 339 14 STRUCTURAL QUALITY ASSURANCE ............................... 341 Roman A. Laskowski 15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES: VALIDATION AS AN ACTIVE TOOL ................... 377 Jane S. Richardson and David С. Richardson 16 STRUCTURE COMPARISON AND ALIGNMENT ......................... 397 Marc A. Marti-Renom, Emidio Capriotti, Ilya N. Shindyalov, and Philip E. Bourne 17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE .......... 419 Raghu P.R. Metpally and Boojala V.B. Reddy 18 THE CATH DOMAIN STRUCTURE DATABASE ......................... 433 Frances M.G. Pearl, Alison Cuff, and Christine A. Orengo Section IV STRUCTURAL AND FUNCTIONAL ASSIGNMENT .............. 457 19 SECONDARY STRUCTURE ASSIGNMENT ............................. 459 Claus A. Andersen and Burkhard Rost 20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS ................. 485 Stella Veretnik, Jenny Gu, and Shoshana Wodak 21 INFERRING PROTEIN FUNCTION FROM STRUCTURE .................. 515 James D. Watson, Gail J. Bartlett, and Janet M. Thornton 22 STRUCTURAL ANNOTATION OF GENOMES ........................... 539 Adam J. Reid, Corin Yeats, Jonathan Lees, and Christine A. Orengo 23 EVOLUTION STUDIED USING PROTEIN STRUCTURE .................. 559 Song Yang, Ruben Valas, and Philip E. Bourne Section V MACROMOLECULAR INTERACTIONS ....................... 573 24 ELECTROSTATIC INTERACTIONS ................................. 575 Nathan A. Baker and J. Andrew McCammon 25 PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS ............ 593 Timothy Robertson and Gabriele Varani 26 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION ................................... 615 Alfonso Valencia and Florencio Pazos 27 DOCKING METHODS, LIGAND DESIGN, AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA ............................. 633 Natasja Brooijmans Section VI STRUCTURE PREDICTION .............................. 663 28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION .............................. 665 Jenny Gu and Philip E. Bourne 29 PREDICTION OF PROTEIN STRUCTURE IN 1D: SECONDARY STRUCTURE, MEMBRANE REGIONS, AND SOLVENT ACCESSIBILITY ..... 679 Burkhard Rost 30 HOMOLOGY MODELING .......................................... 715 Hanka Venselaar, Elmar Krieger, and Gert Vriend 31 FOLD RECOGNITION METHODS ................................... 733 Adam Godzik 32 DE NOVO PROTEIN STRUCTURE PREDICTION: METHODS AND APPLICATION ................................................ 755 Kevin Drew, Dylan Chivian, and Richard Bonneau 33 RNA STRUCTURAL BIOINFORMATICS .............................. 791 Magdalena A. Jonikas, Alain Laederach, and Russ B. Altman Section VII THERAPEUTIC DISCOVERY ............................ 807 34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY ................ 809 William R. Pitt, Alicia Perez Higueruelo, and Colin R. Groom 35 B-CELL EPITOPE PREDICTION .................................. 847 Julia V. Ponomarenko and Marc H.V. van Regenmortel Section VIII FUTURE CHALLENGES ................................ 879 36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS ................................................... 881 Marialuisa Pellegrini-Calace and Janet M. Thornton 37 PROTEIN MOTION: SIMULATION ................................. 907 Han Samish, Jenny Gu, and Michael L. Klein 38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS .................................... 937 Jenny Gu and Vincent J. Hilser 39 PROTEIN DESIGNABILITY AND ENGINEERING ...................... 961 Nikolay V. Dokholyan 40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES ............... 983 Stephen K. Burley, Steven C. Almo, Jeffrey B. Bonanno, Mark R. Chance, Spencer Emtage, Andras Fiser, Andrej Sali, J. Michael Sauder, and Subramanyam Swaminathan INDEX ........................................................ 1019