By Christine A. Orengo, Alex Bateman, Vladimir Uversky
New insights into the evolution and nature of proteins
Exploring a number of precise methods, this publication describes the equipment for evaluating protein sequences and protein constructions so one can establish homologous relationships and classify proteins and protein domain names into evolutionary households. Readers will detect the typical positive factors in addition to the most important philosophical ameliorations underlying the main protein class structures, together with Pfam, Panther, SCOP, and CATH. additionally, they're going to detect how those structures can be utilized to appreciate the evolution of protein households in addition to comprehend and are expecting the measure to which structural and sensible details are shared among family members in a protein family members.
Edited and authored via top overseas specialists, Protein households offers new insights into protein households which are very important to clinical study in addition to protein households that support us comprehend organic platforms and key organic approaches akin to phone signaling and the immune reaction. The e-book is split into 3 sections:
- Section I: strategies Underlying Protein relatives Classification reports the most important options for settling on homologous proteins and classifying them into families.
- Section II: In-Depth studies of Protein households focuses on a few interesting great protein households for which we've got mammoth quantities of series, structural and sensible facts, making it attainable to track the emergence of functionally various relatives.
- Section III: assessment of Protein households in vital organic Systems examines protein households linked to a selected organic topic, equivalent to the cytoskeleton.
All chapters are largely illustrated, together with depictions of evolutionary relationships. References on the finish of every bankruptcy consultant readers to unique learn papers and reports within the box.
Covering protein kin category platforms along precise descriptions of decide upon protein households, this e-book bargains biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new perception into the evolution and nature of proteins.Content:
Chapter 1 computerized Sequence‐Based methods for picking out area households (pages 1–24): Liisa Holm and Andreas Heger
Chapter 2 series class of Protein households: Pfam and different assets (pages 25–36): Alex Bateman
Chapter three Classifying Proteins into area constitution households (pages 37–68): Alison Cuff, Alexey Murzin and Christine Orengo
Chapter four Structural Annotations of Genomes with Superfamily and G3D (pages 69–97): Julian Gough, Corin Yeats and Christine Orengo
Chapter five Phylogenomic Databases and Orthology Prediction (pages 99–124): Kimmen Sjölander
Chapter 6 The Nucleophilic assault Six‐Bladed β‐Propeller (N6P) Superfamily (pages 125–158): Michael A. Hicks, Alan E. Barber and Patricia C. Babbitt
Chapter 7 practical variety of the HUP area Superfamily (pages 159–189): Benoit H. Dessailly and Christine Orengo
Chapter eight The NAD Binding area and the Short‐Chain Dehydrogenase/Reductase (SDR) Superfamily (pages 191–206): Nicholas Furnham, Gemma L. Holliday and Janet M. Thornton
Chapter nine The Globin relations (pages 207–235): Arthur M. Lesk and Juliette T.J. Lecomte
Chapter 10 practical version and Plasticity in Cytoskeletal Protein domain names: classes from the Erythrocyte version (pages 237–284): Anthony J. Baines
Chapter eleven strange Species Distribution and Horizontal move of Peptidases (pages 285–314): Neil D. Rawlings
Chapter 12 Deducing delivery Protein Evolution in keeping with series, constitution, and serve as (pages 315–339): Steven T. Wakabayashi, Maksim A. Shlykov, Ujjwal Kumar, Vamsee S. Reddy, Ankur Malhotra, Erik L. Clarke, Jonathan S. Chen, Rostislav Castillo, Russell de l. a. Mare, Eric I. sunlight and Milton H. Saier
Chapter 14 households of Sequence‐Specific DNA‐Binding domain names in Transcription elements around the Tree of lifestyles (pages 383–420): Varodom Charoensawan and Sarah Teichmann
Chapter 15 Evolution of Eukaryotic Chromatin Proteins and Transcription elements (pages 421–502): L. Aravind, Vivek Anantharaman, Saraswathi Abhiman and Lakshminarayan M. Iyer
Chapter thirteen CRISPR‐Cas platforms and Cas Protein households (pages 341–381): Kira S. Makarova, Daniel H. Haft and Eugene V. Koonin
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Extra resources for Protein Families: Relating Protein Sequence, Structure, and Function
A. (2002) An efﬁcient algorithm for large-scale detection of protein families. Nucleic Acids Res, 30, 1575–1584. J. A. (2000) GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics, 16, 451–457. , Forslund, K. et al. (2010) The Pfam protein families database. Nucleic Acids Res, 38, D211–D222. M. (1970) Distinguishing homologous from analogous proteins. Syst Zool, 19, 99–113. , Fitzgerald, S. et al. (2011) Ensembl 2011. Nucleic Acids Res, 39, D800–D806. J. and Dueck, D.
Forslund, K. et al. (2010) The Pfam protein families database. Nucleic Acids Res, 38, D211–D222. M. (1970) Distinguishing homologous from analogous proteins. Syst Zool, 19, 99–113. , Fitzgerald, S. et al. (2011) Ensembl 2011. Nucleic Acids Res, 39, D800–D806. J. and Dueck, D. (2007) Clustering by passing messages between data points. Science, 315, 972–976. L. (2006) Improving the speciﬁcity of high-throughput ortholog prediction. BMC Bioinformatics, 7, 270. V. S. (2003) Prediction of protein domain boundaries from sequence alone.
2 Domain Decomposition ADDA’s model is conceptually straightforward. In an ideal world, alignments would begin and stop exactly at domain boundaries, if no two proteins shared the same domain combination in the same order. In this ideal world, a multiple alignment built from a sequence database search with a multidomain protein exhibited a block structure (Fig. 2a and c) as a result of its domain composition. In the real world, the block structure is confused by various types of noise (Fig. 2b and d): Multidomain Proteins.
Protein Families: Relating Protein Sequence, Structure, and Function by Christine A. Orengo, Alex Bateman, Vladimir Uversky