STRUCTURAL BIOINFORMATICSPDF电子书下载

Section Ⅰ INTRODUCTION 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 75

5 MACROMOLECULAR STRUCTURE DETERMINATION BY NMR SPECTROSCOPY&John L.Markley，Eldon L.Ulrich，William M.Westler，and Brian F.Volkman 89

6 ELECTRON MICROSCOPY&Niels Volkmann and Dorit Hanein 115

7 MOLECULAR VISUALIZATION&John Tate 135

Section Ⅱ DATA REPRESENTATION AND DATABASES 159

8 THE PDB FORMAT，MMCIF FORMATS，AND OTHER DATA FORMATS&John D.Westbrook and P.M.D.Fitzgerald 161

9 THE PROTEIN DATA BANK&The PDB Team 181

10 THE NUCLEIC ACID DATABASE&Helen M.Berman，John Westbrook，Zukang Feng，Lisa Iype，Bohdan Schneider，and Christine Zardecki 199

11 OTHER STRUCTURE-BASED DATABASES&Helge Weissig and Philip E.Bourne 217

Section Ⅲ COMPARATIVE FEATURES 237

12 PROTEIN STRUCTURE EVOLUTION AND THE SCOP DATABASE&Boojala V.B.Reddy and Philip E.Bourne 239

13 THE CATH DOMAIN STRUCTURE DATABASE&C.A.Orengo，F.M.G.Pearl，and J.M.Thornton 249

14 STRUCTURAL QUALITY ASSURANCE&Roman A.Laskowski 273

15 ALL-ATOM CONTACTS：A NEW APPROACH TO STRUCTURE VALIDATION&Jane S.Richardson 305

16 STRUCTURE COMPARISON AND ALIGNMENT&Philip E.Bourne and Ilya N.Shindyalov 321

Section Ⅳ STRUCTURE AND FUNCTIONAL ASSIGNMENT 339

17 SECONDARY STRUCTURE ASSIGNMENT&Claus A.F.Andersen and Burkhard Rost 341

18 IDENTIFYING STRUCTURAL DOMAINS IN PROTEINS&Lorenz Wernisch and Shoshana J.Wodak 365

19 INFERRING PROTEIN FUNCTION FROM STRUCTURE&Gail J.Bartlett，Annabel E.Todd，and Janet M.Thornton 387

Section Ⅴ PROTEIN INTERACTIONS 409

20 PREDICTION OF PROTEIN-PROTEIN INTERACTIONS FROM EVOLUTIONARY INFORMATION&Alfonso Valencia and Florencio Pazos 411

21 ELECTROSTATIC INTERACTIONS&Nathan A.Baker and J.Andrew McCammon 427

Section Ⅵ PROTEINS AS DRUG TARGETS 441

22 PRINCIPLES AND METHODS OF DOCKING AND LIGAND DESIGN&J.Krumrine，F.Raubacher，N.Brooijmans，and I.Kuntz 443

23 STRUCTURAL BIOINFORMATICS IN DRUG DISCOVERY&Eric B.Fauman，Andrew L.Hopkins，and Colin R.Groom 477

Section Ⅶ STRUCTURE PREDICTION 499

24 CASP AND CAFASP EXPERIMENTS AND THEIR FINDINGS&Philip E.Bourne 501

25 HOMOLOGY MODELING&Elmar Krieger，Sander B.Nabuurs，and Gert Vriend 509

26 FOLD RECOGNITION METHODS&Adam Godzik 525

27 AB INITIO METHODS&Dylan Chivian，Timothy Robertson，Richard Bonneau，and David Baker 547

28 PREDICTION IN 1D：SECONDARY STRUCTURE，MEMBRANE HELICES，AND ACCESSIBILITY&Burkhard Rost 559

Section Ⅷ THE FUTURE 589

29 STRUCTURAL GENOMICS&Stephen K.Burley and Jeffrey B.Bonanno 591

INDEX 613