Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking

Journal of Molecular Biology

Volumn 311, Issue 2, 2001, Pages 395-408

  Aloy, Patrick ^a,b   Querol, Enrique ^a   Aviles, Francesc X ^a   Sternberg, Michael J E ^b  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Active sites; Bioinformatics; Protein function prediction; Structural genomics

Indexed keywords

DNA; PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CLUSTER ANALYSIS; DNA BINDING; EVOLUTION; GENOME; INHERITANCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; VALIDATION PROCESS;

EID: 0035838976     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4870     Document Type: Article

References (46)

1. Predicting function: From genes to genomes and back
2. Predicting functions from protein sequences - Where are the bottlenecks
3. Supersites within superfolds - Binding site similarity in the absence of homology
4. The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
5. Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
6. Practical limits of function prediction
7. Protein annotation: Detective work for function prediction
8. Errors in genome annotation
9. The Pfam protein families database
10. SMART: A web-based tool for the study of genetically mobile domains
11. The SWISS-Prot protein sequence database and its supplement TrEMBL in 2000
12. Increased coverage of protein families with the Blocks Database servers
13. SCOP: A structural classification of proteins database
14. A method to predict functional residues in proteins
15. Identification of functional residues and secondary structure from protein multiple sequence alignment
16. Analysis and prediction of functional sub-types from protein sequence alignments
17. Evolutionarily conserved G alpha beta gamma binding surfaces support a model of the G protein-receptor complex
18. An evolutionary trace method defines binding surfaces common to protein families
19. Identification of functional surfaces of the zinc binding domains of intracellular receptors
20. Evolutionarily conserved pathways of energetic connectivity in protein families
21. Co-evolution of proteins with their interaction partners
22. Structural genomics: Beyond the human genome project
23. Modeling repressor proteins docking to DNA
24. Modelling protein docking using shape complementarity, electrostatics and biochemical information
25. Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
26. Use of pair potentials across protein interfaces in screening predicted docked complexes
27. The protein data bank
28. Obstruct: A program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
29. Selection of representative protein data sets
30. Removing near-neighbour redundancy from large protein sequence collections
31. Basic local alignment search tool
32. Assessing sequence comprison methods with reliable structurally identified distant evolutionary relationships
33. Clustalw: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
34. Evaluation of Gramm low-resolution docking methodology on the hemagglutinin-antibody complex
35. Examination of shape complementarity in docking of unbound proteins
36. Protein docking using spherical polar Fourier correlations
37. Monty: A Monte Carlo approach to protein-DNA recognition
38. Protein docking and complementarity
39. Escher: A new docking procedure applied to the reconstruction of protein tertiary structure
40. Predictive docking of protein-protein and protein-DNA complexes
41. Analysis of protein-protein interaction sites using surface patches
42. Comparitive analysis of multiple protein-sequence alignment methods
43. The complete genome sequence of Escherichia coli K-12
44. Gapped BLAST and PSI-BLAST: A new generation of protein data base search programs