Crossref
journal-article
Elsevier BV
Current Opinion in Structural Biology (78)
References
54
Referenced
67
10.1073/pnas.80.3.726
/ Proc Natl Acad Sci USA / Rapid similarity searches of nucleic acid and protein data banks by Wilbur (1983)10.1126/science.2983426
/ Science / Rapid and sensitive protein similarity searches by Lipman (1985)10.1016/S0022-2836(05)80360-2
/ J Mol Biol / Basic local alignment search tool by Altschul (1990)10.1093/nar/25.17.3389
/ Nucleic Acids Res / Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul (1997)10.1016/j.cbpa.2003.12.004
/ Curr Opin Chem Biol / Protein sequence databases by Apweiler (2004)10.1093/nar/gki063
/ Nucleic Acids Res / GenBank by Benson (2005)10.1126/science.6304883
/ Science / Simian sarcoma virus onc gene, v-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor by Doolittle (1983)10.1126/science.273.5275.595
/ Science / Mapping the protein universe by Holm (1996)10.1016/S0959-440X(96)80058-3
/ Curr Opin Struct Biol / Surprising similarities in structure comparison by Gibrat (1996)10.1016/S0969-2126(97)00260-8
/ Structure / CATH–a hierarchic classification of protein domain structures by Orengo (1997)10.1093/nar/25.1.236
/ Nucleic Acids Res / SCOP: a structural classification of proteins database by Hubbard (1997)10.1016/S0022-2836(66)80258-9
/ J Mol Biol / An improved method of testing for evolutionary homology by Fitch (1966)10.1073/pnas.85.8.2444
/ Proc Natl Acad Sci USA / Improved tools for biological sequence comparison by Pearson (1988)10.1016/0022-2836(81)90087-5
/ J Mol Biol / Identification of common molecular subsequences by Smith (1981)10.1073/pnas.87.6.2264
/ Proc Natl Acad Sci USA / Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes by Karlin (1990)10.1007/BF02458620
/ Bull Math Biol / Maximum-likelihood-estimation of the statistical distribution of Smith-Waterman local sequence similarity scores by Mott (1992)10.1006/jmbi.1997.1525
/ J Mol Biol / Empirical statistical estimates for sequence similarity searches by Pearson (1998)10.1006/jsbi.2001.4393
/ J Struct Biol / 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? by Lupas (2001)10.1016/S0022-2836(02)01371-2
/ J Mol Biol / COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance by Sadreyev (2003)10.1093/bioinformatics/bth090
/ Bioinformatics / A comparison of scoring functions for protein sequence profile alignment by Edgar (2004)10.1002/prot.20184
/ Proteins / Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods by Ohlson (2004)10.1016/j.jmb.2004.12.032
/ J Mol Biol / Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures by Kolodny (2005)10.1002/prot.10543
/ Proteins / Assessment of homology-based predictions in CASP5 by Tramontano (2003)10.1002/prot.10591
/ Proteins / Comparative modeling in CASP5: progress is evident, but alignment errors remain a significant hindrance by Venclovas (2003)10.1002/pro.5560040613
/ Protein Sci / Comparison of methods for searching protein sequence databases by Pearson (1995){'key': '10.1016/j.sbi.2005.05.005_bib26', 'first-page': '145', 'article-title': 'Using video-oriented instructions to speed up sequence comparison', 'volume': '13', 'author': 'Wozniak', 'year': '1997', 'journal-title': 'Comput Appl Biosci'}
/ Comput Appl Biosci / Using video-oriented instructions to speed up sequence comparison by Wozniak (1997)10.1093/bioinformatics/16.8.699
/ Bioinformatics / Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors by Rognes (2000)10.1073/pnas.2533904100
/ Proc Natl Acad Sci USA / The compositional adjustment of amino acid substitution matrices by Yu (2003)10.1073/pnas.84.13.4355
/ Proc Natl Acad Sci USA / Profile analysis: detection of distantly related proteins by Gribskov (1987)10.1006/jmbi.1994.1104
/ J Mol Biol / Hidden Markov models in computational biology. Applications to protein modeling by Krogh (1994){'key': '10.1016/j.sbi.2005.05.005_bib31', 'first-page': '95', 'article-title': 'Hidden Markov models for sequence analysis: extension and analysis of the basic method', 'volume': '12', 'author': 'Hughey', 'year': '1996', 'journal-title': 'Comput Appl Biosci'}
/ Comput Appl Biosci / Hidden Markov models for sequence analysis: extension and analysis of the basic method by Hughey (1996)10.1093/bioinformatics/14.9.755
/ Bioinformatics / Profile hidden Markov models by Eddy (1998)10.1002/pro.5560060319
/ Protein Sci / Embedding strategies for effective use of information from multiple sequence alignments by Henikoff (1997)10.1093/nar/gkh121
/ Nucleic Acids Res / The Pfam protein families database by Bateman (2004)10.1093/nar/gkh117
/ Nucleic Acids Res / The SUPERFAMILY database in 2004: additions and improvements by Madera (2004)10.1093/bioinformatics/15.12.1000
/ Bioinformatics / IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices by Schaffer (1999)10.1093/nar/29.14.2994
/ Nucleic Acids Res / Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements by Schaffer (2001)10.1006/jmbi.1999.2653
/ J Mol Biol / Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches by Aravind (1999)10.1006/jmbi.1998.2221
/ J Mol Biol / Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods by Park (1998)10.1093/nar/24.19.3836
/ Nucleic Acids Res / Searching databases of conserved sequence regions by aligning protein multiple-alignments by Pietrokovski (1996)10.1110/ps.9.2.232
/ Protein Sci / Comparison of sequence profiles. Strategies for structural predictions using sequence information by Rychlewski (2000)10.1006/jmbi.2001.5293
/ J Mol Biol / Within the twilight zone: a sensitive profile-profile comparison tool based on information theory by Yona (2002)10.1093/bioinformatics/bth091
/ Bioinformatics / COACH: profile-profile alignment of protein families using hidden Markov models by Edgar (2004)10.1110/ps.03197403
/ Protein Sci / Profile-profile comparisons by COMPASS predict intricate homologies between protein families by Sadreyev (2003)10.1002/prot.10565
/ Proteins / Using evolutionary information for the query and target improves fold recognition by Wallner (2004)10.1093/protein/11.9.739
/ Protein Eng / Protein structure alignment by incremental combinatorial extension (CE) of the optimal path by Shindyalov (1998)10.1073/pnas.95.11.5913
/ Proc Natl Acad Sci USA / A unified statistical framework for sequence comparison and structure comparison by Levitt (1998)10.1073/pnas.95.11.6073
/ Proc Natl Acad Sci USA / Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships by Brenner (1998)10.1109/JPROC.2002.805303
/ Proc IEEE / Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison by Green (2002)10.1110/ps.03335004
/ Protein Sci / Detection of homologous proteins by an intermediate sequence search by John (2004)10.1110/ps.03328504
/ Protein Sci / Sensitivity and selectivity in protein structure comparison by Sierk (2004)10.1110/ps.03601504
/ Protein Sci / Scoring profile-to-profile sequence alignments by Wang (2004)10.1093/nar/gkf544
/ Nucleic Acids Res / A comparison of profile hidden Markov model procedures for remote homology detection by Madera (2002)10.1016/0888-7543(91)90071-L
/ Genomics / Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms by Pearson (1991)
Dates
Type | When |
---|---|
Created | 20 years, 3 months ago (May 25, 2005, 4:41 a.m.) |
Deposited | 6 years, 7 months ago (Jan. 25, 2019, 10:56 p.m.) |
Indexed | 1 day, 3 hours ago (Aug. 30, 2025, 1:04 p.m.) |
Issued | 20 years, 2 months ago (June 1, 2005) |
Published | 20 years, 2 months ago (June 1, 2005) |
Published Print | 20 years, 2 months ago (June 1, 2005) |
@article{Pearson_2005, title={The limits of protein sequence comparison?}, volume={15}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/j.sbi.2005.05.005}, DOI={10.1016/j.sbi.2005.05.005}, number={3}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Pearson, William R and Sierk, Michael L}, year={2005}, month=jun, pages={254–260} }