LEADER 05701nam 2200757 450 001 9910139014903321 005 20220620111506.0 010 $a1-118-74281-8 010 $a1-118-74308-3 010 $a1-118-74285-0 035 $a(CKB)2550000001163204 035 $a(EBL)1557275 035 $a(OCoLC)863673296 035 $a(SSID)ssj0001061539 035 $a(PQKBManifestationID)11634197 035 $a(PQKBTitleCode)TC0001061539 035 $a(PQKBWorkID)11111126 035 $a(PQKB)10693135 035 $a(OCoLC)868914793 035 $a(MiAaPQ)EBC1557275 035 $a(DLC) 2013018069 035 $a(Au-PeEL)EBL1557275 035 $a(CaPaEBR)ebr10804847 035 $a(CaONFJC)MIL545342 035 $a(EXLCZ)992550000001163204 100 $a20130423h20142014 uy 0 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 00$aProtein families $erelating protein sequence, structure, and function /$fedited by Christine A. Orengo, Alex Bateman 210 1$aHoboken, New Jersey :$cWiley,$d[2014] 210 4$dİ2014 215 $a1 online resource (567 p.) 225 0 $aWiley series in protein and peptide science ;$v10 300 $aIncludes index. 311 $a0-470-62422-1 311 $a1-306-14091-9 327 $aCover; Title Page; Contents; Introduction; Contributors; Part I Concepts Underlying Protein Family Classification; Chapter 1 Automated Sequence-Based Approaches for Identifying Domain Families; 1.1 Introduction; 1.2 Motivation Behind Automated Classification; 1.3 Clustering the Sequence Space Graph; 1.4 Historical Overview of Sequence Clustering Algorithms; 1.5 Related Methods; 1.6 Quality Assessment; 1.7 ADDA-The Automatic Domain Delineation Algorithm; 1.8 Results; 1.9 Conclusions; References; Chapter 2 Sequence Classification of Protein Families: Pfam and other Resources; 2.1 Introduction 327 $a2.2 Pfam2.3 Smart, Prosite Profiles, CDD and Tigrfams; 2.4 Philosophy of Pfam; 2.5 HMMER3 and Jackhmmer; 2.6 Sources of New Families; 2.7 Annotation of Families; 2.8 The InterPro Collection; 2.9 The Future of Sequence Classification; References; Chapter 3 Classifying Proteins into Domain Structure Families; 3.1 Introduction; 3.2 The Classification Hierarchies Adopted by Scop and Cath; 3.3 Challenges in Identifying Domains in Proteins; 3.4 Structure-Based Approaches for Identifying Related Folds and Homologs; 3.5 Approaches to Structure Comparison; 3.6 The DALI Algorithm 327 $a3.7 The SSAP Algorithm Used for Fold Recognition in CATH3.8 Fast Approximate Methods Used to Recognize Folds in CATH; 3.9 Measuring Structural Similarity; 3.10 Multiple Structure Alignment; 3.11 Classification Protocols; 3.12 Population of the Hierarchy; 3.13 Comparisons Between Scop and CATH; 3.14 Hierarchical Classifications Versus Structural Continuum; 3.15 Websites; References; Chapter 4 Structural Annotations of Genomes with Superfamily and Gene3D; 4.1 Introduction; 4.2 The Importance of Being High Throughput; 4.3 The Use of Structural Information; 4.4 Applications; 4.5 History 327 $a4.6 Technology4.7 Hidden Markov Models; 4.8 Building Models; 4.9 Domain Annotations; 4.10 High Throughput Computation; 4.11 Development of New Bioinformatics Algorithms; 4.12 Genomes; 4.13 e-Value Scores; 4.14 Other Sequence Sets; 4.15 Data Access; 4.16 Analysis Tools; 4.17 Conclusion; References; Chapter 5 Phylogenomic Databases and Orthology Prediction; 5.1 The Evolution of Novel Functions and Structures in Gene Families; 5.2 Homologs, Orthologs, Paralogs, and Other Evolutionary Terms; 5.3 The Standard Functional Annotation Protocol; 5.4 Orthology Identification Methods and Databases 327 $a5.5 Challenges in Phylogenetic Methods of Ortholog Identification5.6 Evaluating Ortholog Identification Methods; 5.7 Orthology Databases; 5.8 Phylogenomic Databases; 5.9 PhyloFacts; 5.10 Subfamily Classification in Phylofacts; 5.11 PhyloFacts 3.0; 5.12 PhylomeDB; 5.13 Panther; 5.14 Structural Phylogenomics: Improved Functional Annotation Through Integration of Information from Structure and Evolution; 5.15 Specific Issues in Phylogenomic Pipelines; 5.16 Improving Functional Inference using Information from Protein Structure; 5.17 Example Case Studies; 5.18 Review of Key Points; References 327 $aPart II In-Depth Reviews of Protein Families 330 $a"This book describes approaches for recognizing and classifying proteins into families of evolutionary related proteins. Reviewing all the major resources for classifying protein families, the book combines descriptions of general philosophies of protein family classification systems with detailed descriptions and examples of selected families found in different biological systems. Scientists in diverse areas of biology and protein science will learn how to use the various resources and databases and gain valuable insight into how proteins evolve and how new functional repertoires emerge"--$cProvided by publisher. 410 0$aWiley Series in Protein and Peptide Science 606 $aProteins 606 $aProteomics 606 $aMolecular biology$xData processing 606 $aBioinformatics 615 0$aProteins. 615 0$aProteomics. 615 0$aMolecular biology$xData processing. 615 0$aBioinformatics. 676 $a572/.6 686 $aCOM082000$2bisacsh 701 $aOrengo$b Christine A.$f1955-$0961782 701 $aBateman$b Alex$f1972-$0961783 801 0$bMiAaPQ 801 1$bMiAaPQ 801 2$bMiAaPQ 906 $aBOOK 912 $a9910139014903321 996 $aProtein families$92180400 997 $aUNINA