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STRUCTURAL BIOINFORMATICS SECOND EDITION
STRUCTURAL BIOINFORMATICS SECOND EDITION

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  • 电子书积分:26 积分如何计算积分?
  • 作 者:
  • 出 版 社:WILEY BLACKWELL
  • 出版年份:2009
  • ISBN:0470181058
  • 页数:1035 页
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《STRUCTURAL BIOINFORMATICS SECOND EDITION》目录
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Section Ⅰ DATA COLLECTION,ANALYSIS,AND VISUALIZATION 1

1 DEFINING BIOINFORMATICS AND STRUCTURAL BIOINFORMATICS&Russ B.Altman and Jonathan M.Dugan 3

2 FUNDAMENTALS OF PROTEIN STRUCTURE&Eric D.Scheeff and J.Lynn Fink 15

3 FUNDAMENTALS OF DNA AND RNA STRUCTURE&Stephen Neidle,Bohdan Schneider,and Helen M.Berman 41

4 COMPUTATIONAL ASPECTS OF HIGH-THROUGHPUT CRYSTALLOGRAPHIC MACROMOLECULAR STRUCTURE DETERMINATION&Paul D.Adams,Ralf W.Grosse-Kunstleve,and Axel T.Brunger 77

5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY&John L.Markley,Arash Bahrami,Hamid R.Eghbalnia,Francis C.Peterson,Robert C.Tyler,Eldon L.Ulrich,William M.Westler,and Brian F.Volkman 93

6 ELECTRON MICROSCOPY IN THE CONTEXT OF STRUCTURAL SYSTEMS BIOLOGY&Niels Volkmann and Dorit Hanein 143

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&Sheng Li,Dmitri Mouradov,Gordon King,Tong Liu,Ian Ross,Bostjan Kobe,Virgil L.Woods Jr,and Thomas Huber 171

8 SEARCH AND SAMPLING IN STRUCTURAL BIOINFORMATICS&Ilan Samish 207

9 MOLECULAR VISUALIZATION&Steven Bottomley and Erik Helmerhorst 237

Section Ⅱ DATA REPRESENTATION AND DATABASES 269

10 THE PDB FORMAT,MMCIF FORMATS,AND OTHER DATA FORMATS&John D.Westbrook and Paula M.D.Fitzgerald 271

11 THE WORLDWIDE PROTEIN DATA BANK&Helen M.Berman,Kim Henrick,Haruki Nakamura,and John L.Markley 293

12 THE NUCLEIC ACID DATABASE&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 305

13 OTHER STRUCTURE-BASED DATABASES&J.Lynn Fink,Helge Weissig,and Philip E.Bourne 321

Section Ⅲ DATA INTEGRITY AND COMPARATIVE FEATURES 339

14 STRUCTURAL QUALITY ASSURANCE&Roman A.Laskowski 341

15 THE IMPACT OF LOCAL ACCURACY IN PROTEIN AND RNA STRUCTURES:VALIDATION AS AN ACTIVE TOOL&Jane S.Richardson and David C.Richardson 377

16 STRUCTURE COMPARISON AND ALIGNMENT&Marc A.Marti-Renom,Emidio Capriotti,Ilya N.Shindyalov,and Philip E.Bourne 397

17 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE&Raghu P.R.Metpally and Boojala V.B.Reddy 419

18 THE CATH DOMAIN STRUCTURE DATABASE&Frances M.G.Pearl,Alison Cuff,and Christine A.Orengo 433

Section Ⅳ STRUCTURAL AND FUNCTIONAL ASSIGNMENT 457

19 SECONDARY STRUCTURE ASSIGNMENT&Claus A.Andersen and Burkhard Rost 459

20 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS&Stella Veremik,Jenny Gu,and Shoshana Wodak 485

21 INFERRING PROTEIN FUNCTION FROM STRUCTURE&James D.Watson,Gail J.Bartlett,and Janet M.Thornton 515

22 STRUCTURAL ANNOTATION OF GENOMES&Adam J.Reid,Corin Yeats,Jonathan Lees,and Christine A.Orengo 539

23 EVOLUTION STUDIED USING PROTEIN STRUCTURE&Song Yang,Ruben Valas,and Philip E.Bourne 559

Section Ⅴ MACROMOLECULAR INTERACTIONS 573

24 ELECTROSTATIC INTERACTIONS&Nathan A.Baker and J.Andrew McCammon 575

25 PREDICTION OF PROTEIN-NUCLEIC ACID INTERACTIONS&Timothy Robertson and Gabriele Varani 593

26 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION&Alfonso Valencia and Florencio Pazos 615

27 DOCKING METHODS,LIGAND DESIGN,AND VALIDATING DATA SETS IN THE STRUCTURAL GENOMICS ERA&Natasja Brooijmans 633

Section Ⅵ STRUCTURE PREDICTION 663

28 CASP AND OTHER COMMUNITY-WIDE ASSESSMENTS TO ADVANCE THE FIELD OF STRUCTURE PREDICTION&Jenny Gu and Philip E.Bourne 665

29 PREDICTION OF PROTEIN STRUCTURE IN 1D:SECONDARY STRUCTURE,MEMBRANE REGIONS,AND SOLVENT ACCESSIBILITY&Burkhard Rost 679

30 HOMOLOGY MODELING&Hanka Venselaar,Elmar Krieger,and Gert Vriend 715

31 FOLD RECOGNITION METHODS&Adam Godzik 733

32 DE NOVO PROTEIN STRUCTURE PREDICTION:METHODS AND APPLICATION&Kevin Drew,Dylan Chivian,and Richard Bonneau 755

33 RNA STRUCTURAL BIOINFORMATICS&Magdalena A.Jonikas,Alain Laederach,and Russ B.Altman 791

Section Ⅶ THERAPEUTIC DISCOVERY 807

34 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY&William R.Pitt,Alicia Perez Higueruelo,and Colin R.Groom 809

35 B-CELL EPITOPE PREDICTION&Julia V.Ponomarenko and Mare H.V.van Regenmortel 847

Section Ⅷ FUTURE CHALLENGES 879

36 METHODS TO CLASSIFY AND PREDICT THE STRUCTURE OF MEMBRANE PROTEINS&Marialuisa Pellegrini-Calace and Janet M.Thornton 881

37 PROTEIN MOTION:SIMULATION&Ilan Samish,Jenny Gu,and Michael L.Klein 907

38 THE SIGNIFICANCE AND IMPACTS OF PROTEIN DISORDER AND CONFORMATIONAL VARIANTS&Jenny Gu and Vincent J.Hilser 937

39 PROTEIN DESIGNABILITY AND ENGINEERING&Nikolay V.Dokholyan 961

40 STRUCTURAL GENOMICS OF PROTEIN SUPERFAMILIES&Stephen K.Burley,Steven C.Almo,Jeffrey B.Bonanno,Mark R.Chance,Spencer Emtage,Andras Fiser,Andrej Sali,J.Michael Sauder,and Subramanyam Swaminathan 983

INDEX 1019

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