Protein Families Relating Protein Sequence, Structure, and Function

CHRISTINE ORENGO, PhD, is Professor of Bioinformatics at University College London. Dr. Orengo's research focuses on protein structure comparison, classification, and analysis. Her group develops the CATH domain family classification and algorithms for predicting protein functions and functional networks.

ALEX BATEMAN, PhD, is Senior Investigator at Wellcome Trust Sanger Institute, where he leads the Pfam database project. Dr. Bateman also participates in the European InterPro project, which seeks to merge the annotations from Pfam, PRINTS, Prosite, and other domain databases.

Introduction. Christine Orengo and Alex Bateman

Section 1. Concepts underlying protein family classification

1. Automated sequence based approaches for identifying domain families
Liisa Holm and Andreas Heger

2. Sequence classification of protein families: Pfam and other resources
Alex Bateman

3. Classifying proteins into domain structure families
Alison Cuff, Alexey G. Murzin and Christine Orengo

4. Structural annotations of genomes with SUPERFAMILY and Gene3D
Julian Gough, Corin Yeats and Christine Orengo

5. Phylogenomic databases and orthology prediction
Kimmen Sjölander

Section 2. In depth reviews of protein families

6. The Nucleophilic Attack 6-bladed β-Propeller (N6P) Superfamily
Michael A. Hicks, Alan E. Barber II, and Patricia C. Babbitt

7. Structural elaboration of the HUP domain superfamily
Benoit H. Dessailly and Christine A. Orengo

8. The NAD Binding Domain And The Short-Chain Dehydrogenase/Reductase (SDR) Superfamily
Nicholas Furnham, Gemma L. Holliday & Janet M. Thornton

9. The Globin Family
Arthur M. Lesk and Juliette T.J. Lecomte

Section 3. Review of protein families in important biological systems

10. Functional adaptation and plasticity in cytoskeletal protein domains: Lessons from the erythrocyte model
Anthony J. Baines

11. Unusual species distribution and horizontal transfer of peptidases
Neil D. Rawlings

12. Deducing Transport Protein Evolution Based on Sequence, Structure, and Function
Steven T. Wakabayashi, Maksim A. Shlykov, Ujjwal Kumar, Vamsee S. Reddy, Ankur Malhotra, Erik L. Clarke, Jonathan S. Chen, Rostislav Castillo, Russell De La Mare, Eric I. Sun and Milton H. Saier, Jr

13. CRISPR-Cas systems and Cas protein families
Kira S. Makarova, Daniel H. Haft, Eugene V. Koonin

14. Families of sequence-specific DNA-binding Domains in Transcription Factors across the Tree of Life
Varodom Charoensawan and Sarah Teichmann

15. Evolution of Eukaryotic chromatin proteins and transcription factors
L.Aravind, Vivek Anantharaman, Saraswathi Abhiman and Lakshminarayan M. Iyer

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