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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