PDB_ISL: an intermediate sequence library for protein structure assignment
Pages 283 - 289
Abstract
For large scale structural assignment to sequences, as in computational structural genomics, a fast yet sensitive homology search procedure is essential. A new approach using intermediate sequences was tested as a shortcut to iterative multiple sequence search methods such as PSI-BLAST and hidden Markov models. A library containing potential intermediate sequences for proteins of known structure (PDB_ISL) was constructed. The sequences in the library were collected from a large sequence database using the sequences of the domains of proteins of known structure as the query sequences and the program PSI-BLAST. Sequences of proteins of unknown structure can be matched to distantly related proteins of known structure by using any pairwise sequence comparison methods to find homologues in PDB_ISL. Searches of PDB_ISL were calibrated, and the number of correct matches found at a given error rate was the same as that found by PSI_BLAST. The advantage of this library is that it uses pairwise sequence comparison methods, such as FASTA or BLAST2, and can, therefore, be searched easily and, in many cases, much more quickly than an iterative multiple sequence comparison method. The procedure is roughly twenty times faster than PSI-BLAST for small genomes and several hundred times for large genomes such as C. elegans.
Sequences can be submitted to the PDB_ISL servers at
http://stash.mrc-lmb.cam.ac.uk/PDB_ISL/
ftp://ftp.ebi.ac.uk/pub/databases/pdb_isl/
References
[1]
Altschul, S F, Madden, TL, Schaf'fer, A A, Zhang, J, Zhang, Z, Miller, W., and Lipman, D I, (1997), Gapped BLAST and PSI-BLAST a new generation of protein database search programs Nucleic Acids Res, 25, 3389-3402
[2]
Bateman, A, Burney, E, Durbin, R, Eddy, S R, Finn, R D and Sonnhammer, ELL (1999) Pfam 31 1313 multiple alignments and profile HMMs match the majority of proteins Nucleic Acids Res, 27, 260-262
[3]
Brenner, S E, Chothia C and Hubbard TIP (1998) Assessing sequence comparison methods with reliable structurally identified evolutionary relationships Proc Natl Acad Sci USA, 95, 6073-6078.
[4]
Eddy, S R (1996) Hidden Markov Models Curr Op Struc Biol, 3. 361-365
[5]
Elofsson, A and Sonnhammer, E L (1999) A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinformatics, 15(6), 480-500
[6]
Fischer, D and Eisenberg, D (1997) Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium Proc Natl Acad Sci USA, 94, 11929-11934
[7]
Fraser, C M, Gocayne, J D, White, O, el al, (1995) The minimal gene complement of Mycoplasma genitalium Science, 270, 397-403
[8]
Gerstein. M (1997) A Structural Census of Genomes Comparing Bacterial, Eukaryotic and Archaeal Genomes in Terms of Protein Structure J Mol Biol, 274, 562-576
[9]
Grundy, W N (1998) Homology detection via family pairwise search J Comput Biol, 5(3), 479-491
[10]
Grundy, W N and Bailey, T L (1999) Family pairwise search with embedded motif models Biomformatics, 15(6), 463- 470
[11]
Holm, L. and Sander, C (1998) Removing near-neighbour redundancy from large protein sequence collections Bioinformatics, 14, 423-429.
[12]
Huynen. M. Doerks, T, Eisenhaber, F, Orengo, C, Sunyaev, S. Yuan, Y and Bork, P (1998) Homology-based Fold Predictions for Mycoplasma genitalium proteins J Mol Biol, 280, 323-326
[13]
Janccek. S and Bateman, A (1996) The parallel (a/b)8 bairel Perhaps the most universal and the most puzzling fold Biologia, 51, 613-628.
[14]
Karplus, K, Barrett, C. and Itughcy, R (1999) Hidden Markov Models for Detecting Remote Protein Homologies Bioinformatics, 14, 846-856
[15]
Krogh, A. Blown, M, Mian, IS, Sjolander, K., and Haussler. D (1994) Hidden Markov-Models in Computational Biology- Applications in Protein Modelling J Mol Biol, 235, 1501-1531
[16]
Murzin, A G, Brenner, S E, Hubbard, T and Chothia, C (1995) SCOP A structural classification of proteins database for the investigation of sequences and structures dJ Mol Biol, 247, 536-540
[17]
Park. I. Terchmann, S A, Hubbard, T, and Chothia, C, (1997), Intermediate sequences increase the detection of distant sequence homologies J Mol Biol 273, 349-354.
[18]
Park, I and Teichmann, SA (1998) DIVCLUS an automatic method in the GEANFAMMER package that finds homologous dommns in single- and multi-domain proteins Bioinformatics, 14, 144-150
[19]
Park, I, Karplus, K, Barrett, C, Hughey, R., Haussler, D., Hubbard, T and Chothia, C. (1998) Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods d Moi Biol, 284, 1201-1210.
[20]
Park, J. Holm, L, and Chothia, C (1999) Sequence search algorithms assessment and testing toolkit' SAT Bioinformatics, submitted.
[21]
Pearson. W R. and Lipman, D J, (1988), Improved tools for biological sequence comparison Proc Natl Acad Sci USA, 85(8). 2444-2448
[22]
Rost, B (1998) Marrying structure and genomics Structure, 6, 259-63
[23]
Rychlewski, L, Zhang, B and Godzik, A (1998) Fold and function predictions for Mycoplasma genitalium proteins Folding and design, 3. 229-238.
[24]
Salamov. A A, Suwa, M, Orengo, CA, and Swindells, M B (1999) Genome analysis assigning protein coding regions to three-dimensional structures Protein Sci 8, 771-777
[25]
Sanchez, R and Sali, A (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc Natl Acad Sci USA, 95,13597-13602
[26]
Shapiro. L. and Lima, C D (1998)The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science Structure. 6, 265-267
[27]
Tatusov, R L., Altschul, S F and Kooini, E V (1994) Detection of conserved segments in proteins, iterative scanning of sequence databases with alignment blocks Proc Natl Acad Sci USA, 91, 12091-12095.
[28]
Teichmann, S A, Park, I and Chothia, C (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplication and domain rearrangement Proc Natl Acad Sci USA, 95, 14658-14663.
[29]
Teichmann, S A, Chothia. C. and Gerstein, M (1999) Advances in Structural Genomics. Curr Op Struc Biol, 9, 390-399
[30]
Wolf, Y I, Brenner, S.E, Bash, PA and Koomn, EV (1999) Distribution of protein folds in the three superkingdoms of life Genome Res, 9, 17-26.
[31]
Wootton, JC and Federhen, S (1993) Statistics of local complexity in amino acid sequences and sequences databases Computers and Chemistry 17, 149-163.
[32]
Wilmanns, M, Hyde, C.C., Davies, D R, Kirschner, K and Jansonius, J N (1991) Structural conservation in parallel beta/alpha-barrel enzymes that catlyze three sequential reaction in the pathway of tryptophan biosynthesis Biochemistry, 30, 9161- 9169
- PDB_ISL: an intermediate sequence library for protein structure assignment
Recommendations
High performance computing workflow for protein functional annotation
XSEDE '13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to DiscoveryFunctional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the PSU (Protein Sequence Universe) expands exponentially. Newly sequenced bacterial genomes alone contain over 7.5 ...
In silico identification of putative drug targets in pseudomonas aeruginosa through metabolic pathway analysis
PRIB'07: Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformaticsComparative genomic analysis between pathogens and the host Homo sapiens has led to identification of novel drug targets. Microbial drug target identification and validation has been the latest trend in pharmacoinformatics. In order to identify a ...
Mining Cytochrome b561 proteins from plant genomes
Cytochrome b561 (Cyt-b561) proteins are important for plant growth, development, and prevention of damage to plants. Because of their high sequence divergence, thorough mining of Cyt-b561 proteins from plant genomes are not easy. Currently there is only ...
Comments
Information & Contributors
Information
Published In
April 2000
329 pages
ISBN:1581131860
DOI:10.1145/332306
Copyright © 2000 ACM.
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]
Sponsors
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 08 April 2000
Check for updates
Author Tags
Qualifiers
- Article
Conference
RECOMB00
Sponsor:
Acceptance Rates
Overall Acceptance Rate 148 of 538 submissions, 28%
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- 0Total Citations
- 277Total Downloads
- Downloads (Last 12 months)62
- Downloads (Last 6 weeks)22
Reflects downloads up to 16 Jan 2025
Other Metrics
Citations
View Options
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in