SELECTED BIBLIOGRAPHY

Introduction

• Bork P, Koonin EV.  Predicting functions from protein sequences--where are the bottlenecks? Nat Genet. 1998 Apr;18(4):313-8. Review.
• General.
• Attwood TK. Genomics. The Babel of bioinformatics. Science. 2000 Oct 20;290(5491):471-3.
• General

Homology, Orthology and Paralogy

• Sonnhammer ELL andKoonin EV. Orthology, paralogy and proposed classification for paralog subtypes. TIG. 2002 18(12):619.
• Basic
• Remm M, Storm CE, Sonnhammer EL.  Automatic clustering of orthologs and in-paralogs from pairwise species

comparisons. J Mol Biol. 2001 Dec 14;314(5):1041-52.
• Advanced

Sequence Alignments, Patterns and Profiles.

Sequence alignments

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.
• Basic
• Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. Review.
• Basic

Patterns

• Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P.  PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 2002 Sep;3(3):265-74.
• Basic
• Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A. The PROSITE database, its status in 2002. Nucleic Acids Res. 2002 Jan 1;30(1):235-8.
• Basic

Profiles and HMMs

• Altschul SF, Koonin EV.  Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. Trends Biochem Sci. 1998 Nov;23(11):444-7. Review.
• Basic
• Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14(9):755-63. Review.
• General.

Protein Domains and Families.

Protein domains

• Heger A, Holm L. Picasso: generating a covering set of protein family profiles. Bioinformatics. 2001 Mar;17(3):272-9.
• Advanced
• Heger A, Holm L. Exhaustive enumeration of protein domain families. J Mol Biol. 2003 May 2;328(3):749-67.
• Advanced
• Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res. 2002 Jan 1;30(1):276-80.
• Basic
• Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P.  Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 2002 Jan 1;30(1):242-4.
• Advanced
• Schultz J, Copley RR, Doerks T, Ponting CP, Bork P.  SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res. 2000 Jan 1;28(1):231-4.
• Advanced
• Schultz J, Milpetz F, Bork P, Ponting CP.  SMART, a simple modular architecture research tool: identification of signaling

domains. Proc Natl Acad Sci U S A. 1998 May 26;95(11):5857-64.
• Advanced

Clustering. Protein families

• Tatusov RL, Koonin EV, Lipman DJ.  A genomic perspective on protein families. Science. 1997 Oct 24;278(5338):631-7. Review.
• Basic
• Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000 Jan 1;28(1):33-6.
• Basic
• Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001 Jan 1;29(1):22-8.
• Basic
• Yona G, Linial N, Linial M. ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins. 1999 Nov 15;37(3):360-78.
• Advanced
• Kunin V, Cases I, Enright AJ, de Lorenzo V, Ouzounis CA. Myriads of protein families, and still counting. Genome Biol. 2003;4(2):401.
• General

Protein Function Prediction from Sequence Similarity

Function transfer: limits and errors in function prediction.

• Devos D, Valencia A. Practical limits of function prediction. Proteins. 2000 Oct 1;41(1):98-107.
• Basic
• Doerks T, Bairoch A, Bork P. Protein annotation: detective work for function prediction. Trends Genet. 1998 Jun;14(6):248-50. Review.
• General.

Protein Function Prediction with Methods NOT based on Sequence Similarity.

Protein features

• Jensen LJ, Gupta R, Blom N, Devos D, Tamames J, Kesmir C, Nielsen H, Staerfeldt HH, Rapacki K, Workman C, Andersen CA, Knudsen S, Krogh A, Valencia A, Brunak S. Prediction of human protein function from post-translational modifications and

localization features. J Mol Biol. 2002 Jun 21;319(5):1257-65.
• Advanced.

Structure to function

• Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol. 2000 Mar;18(3):283-7. Review.
• General
• Eisenstein E, Gilliland GL, Herzberg O, Moult J, Orban J, Poljak RJ, Banerjei L, Richardson D, Howard AJ. Biological function made crystal clear - annotation of hypothetical proteins via structural genomics. Curr Opin Biotechnol. 2000 Feb;11(1):25-30. Review.
• General

Comparative sequence genomics

• von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B.  STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003 Jan 1;31(1):258-61.
• Advanced
• von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002 May 23;417(6887):399-403.
• Advanced

Proteomics

• Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol. 2003 Jun;21(6):697-700.
• Advanced

Information extraction

Blaschke C, Hirschman L and Valencia A. (2002) Information extraction in Molecular Biology, Briefings in Bioinformatics 3: 154-165.
• General

Prediction of 1D Features

• Rost, B. (1996). PHD: predicting one-dimensional protein structure byprofile based neural networks. Meth. Enzymol.,266, 525-539.
• Basic
• Sonnhammer, E. L. L., von Heijne, G. & Krogh, A. (1998). A hidden Markov model for predicting transmembrane helices in protein sequences. In Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98)eds.), pp. 175-182.
• Advanced
• Chris Sander and Reinhard Schneider Proteins, Database of homology derived protein structures and the structural meaning of sequence alignment 1991,9, 56-68
• Advanced
• Chothia C. and Lesk A. (EMBO J 1986;5:823-826)
• General

Protein Structure Prediction: Fold Recognition

• Bowie JU, Luthy R, Eisenberg D. 1991 A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164-70.
• Basic
• Manfred J Sippl. Knowledge-based potentials for proteins Current Opinion in Structural Biology 1995, 5:229-235 .
• Advanced
• Bork, P., C. Sander, A. Valencia 1992. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc.Natl.Acad.Sci.USA 89:7290-729.
• Basic
• Pcons: A neural network based consensus predictor that improves fold recognition. Jesper Lundström, Leszek Rychlewski, Janusz Bujnicki and Arne Elofsson, 2001 Protein Science Nov;10(11):2354-62 .
• Advanced

Protein Structure Prediction: Homology Modelling

• A. Sali,  L. Potterton,  F. Yuan,  H. vanVlijmen,  M. Karplus.  Evaluation of comparative protein structure modeling by MODELLER. Proteins 23, 318-326, 1995.
• Basic
• Baker, D., and Sali, A. (2001). Protein structure prediction and structural genomics . Science, Vol 294 No. 5540   pp. 93-6.
• General

The Space of Protein Structure

• Liisa Holm and Chris Sander. Mapping the Protein Universe (1998) 273 (5275) p595
• General - A review of 3D structural comparison.
• A.N. Lupas, C.P. Ponting, R.B. Russell On the Evolution of Protein Folds: Are similar motifs in different protein folds the result of convergence, insertion or relics of an ancient peptide world? J. Struct. Biol., 134,191-203, 2001 .
• Advanced