-
1
-
-
0023989064
-
Improved tools for biological sequence comparison
-
10.1073/pnas.85.8.2444 3162770
-
Improved tools for biological sequence comparison. WR Pearson, DJ Lipman, Proc Natl Acad Sci USA 1988 85 2444 2448 10.1073/pnas.85.8.2444 3162770
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman, Nucleic Acids Res 1997 25 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
67649518035
-
Homology modeling in drug discovery: Current trends and applications
-
10.1016/j.drudis.2009.04.006 19422931
-
Homology modeling in drug discovery: current trends and applications. CN Cavasotto, SS Phatak, Drug Discov Today 2009 14 676 683 10.1016/j.drudis.2009. 04.006 19422931
-
(2009)
Drug Discov Today
, vol.14
, pp. 676-683
-
-
Cavasotto, C.N.1
Phatak, S.S.2
-
4
-
-
77952297501
-
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
-
10.1186/1471-2105-11-146 20307279
-
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments. ML Sierk, ME Smoot, EJ Bass, WR Pearson, BMC Bioinformatics 2010 11 146 10.1186/1471-2105-11-146 20307279
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 146
-
-
Sierk, M.L.1
Smoot, M.E.2
Bass, E.J.3
Pearson, W.R.4
-
5
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
10.1016/0022-2836(70)90057-4 5420325
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins. SB Needleman, CD Wunsch, J Mol Biol 1970 48 443 453 10.1016/0022-2836(70)90057-4 5420325
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
6
-
-
0019887799
-
Identification of common molecular subsequences
-
Identification of common molecular subsequences. TF Smith, MS Waterman, J Mol Evol 1981 147 195 197
-
(1981)
J Mol Evol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
7
-
-
0029046744
-
An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited
-
10.1006/jmbi.1995.0340 7602593
-
An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. G Vogt, T Etzold, P Argos, J Mol Biol 1995 249 816 831 10.1006/jmbi.1995.0340 7602593
-
(1995)
J Mol Biol
, vol.249
, pp. 816-831
-
-
Vogt, G.1
Etzold, T.2
Argos, P.3
-
8
-
-
72549111108
-
Optimizing substitution matrix choice and gap parameters for sequence alignment
-
10.1186/1471-2105-10-396 19954534
-
Optimizing substitution matrix choice and gap parameters for sequence alignment. RC Edgar, BMC Bioinformatics 2009 10 396 10.1186/1471-2105-10-396 19954534
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 396
-
-
Edgar, R.C.1
-
9
-
-
3042550791
-
A comparison of scoring functions for protein sequence profile alignment
-
DOI 10.1093/bioinformatics/bth090
-
A comparison of scoring functions for protein sequence profile alignment. RC Edgar, K Sjölander, Bioinformatics 2004 20 1301 1308 10.1093/bioinformatics/bth090 14962936 (Pubitemid 38807585)
-
(2004)
Bioinformatics
, vol.20
, Issue.8
, pp. 1301-1308
-
-
Edgar, R.C.1
Sjolander, K.2
-
10
-
-
0042594474
-
SATCHMO: Sequence alignment and tree construction using hidden Markov models
-
DOI 10.1093/bioinformatics/btg158
-
SATCHMO: sequence alignment and tree construction using hidden Markov models. RC Edgar, K Sjölander, Bioinformatics 2003 19 1404 1411 10.1093/bioinformatics/btg158 12874053 (Pubitemid 36939819)
-
(2003)
Bioinformatics
, vol.19
, Issue.11
, pp. 1404-1411
-
-
Edgar, R.C.1
Sjolander, K.2
-
11
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
DOI 10.1101/gr.2821705
-
ProbCons: Probabilistic consistency-based multiple sequence alignment. CB Do, MS Mahabhashyam, M Brudno, S Batzoglou, Genome Res 2005 15 330 340 10.1101/gr.2821705 15687296 (Pubitemid 40309398)
-
(2005)
Genome Research
, vol.15
, Issue.2
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.P.2
Brudno, M.3
Batzoglou, S.4
-
12
-
-
33750001271
-
MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
-
DOI 10.1093/nar/gkl514
-
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. J Pei, NV Grishin, Nucleic Acids Res 2006 34 4364 4374 10.1093/nar/gkl514 16936316 (Pubitemid 44567036)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.16
, pp. 4364-4374
-
-
Pei, J.1
Grishin, N.V.2
-
13
-
-
77955352019
-
MSAProbs: Multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
-
10.1093/bioinformatics/btq338 20576627
-
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Y Liu, B Schmidt, DL Maskell, Bioinformatics 2010 26 1958 1964 10.1093/bioinformatics/btq338 20576627
-
(2010)
Bioinformatics
, vol.26
, pp. 1958-1964
-
-
Liu, Y.1
Schmidt, B.2
Maskell, D.L.3
-
14
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
DOI 10.1093/bioinformatics/bti125
-
Protein homology detection by HMM-HMM comparison. J Söding, Bioinformatics 2005 21 951 960 10.1093/bioinformatics/bti125 15531603 (Pubitemid 40467915)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
15
-
-
0029174347
-
Multiple alignment using hidden Markov models
-
7584426
-
Multiple alignment using hidden Markov models. SR Eddy, Proc Int Conf Intell Syst Mol Biol 1995 3 114 120 7584426
-
(1995)
Proc Int Conf Intell Syst Mol Biol
, vol.3
, pp. 114-120
-
-
Eddy, S.R.1
-
16
-
-
0347513228
-
Efficient estimation of emission probabilities in profile hidden Markov models
-
DOI 10.1093/bioinformatics/btg328
-
Efficient estimation of emission probabilities in profile hidden Markov models. V Ahola, T Aittokallio, E Uusipaikka, M Vihinen, Bioinformatics 2003 19 2359 2368 10.1093/bioinformatics/btg328 14668219 (Pubitemid 38016635)
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2359-2368
-
-
Ahola, V.1
Aittokallio, T.2
Uusipaikka, E.3
Vihinen, M.4
-
17
-
-
39449089407
-
Improving model construction of profile HMMs for remote homology detection through structural alignment
-
DOI 10.1186/1471-2105-8-435
-
Improving model construction of profile HMMs for remote homology detection through structural alignment. JS Bernardes, AM Dávila, VS Costa, G Zaverucha, BMC Bioinformatics 2007 8 435 10.1186/1471-2105-8-435 17999748 (Pubitemid 351267360)
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 435
-
-
Bernardes, J.S.1
Davila, A.M.R.2
Costa, V.S.3
Zaverucha, G.4
-
18
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson, DG Higgins, TJ Gibson, Nucleic Acids Res 1994 22 4673 4680 10.1093/nar/22.22.4673 7984417 (Pubitemid 24354800)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
19
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
10.1006/jmbi.2000.4042 10964570
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment. C Notredame, DG Higgins, J Heringa, J Mol Biol 2000 302 205 217 10.1006/jmbi.2000.4042 10964570
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
20
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Amino acid substitution matrices from protein blocks. S Henikoff, JG Henikoff, Proc Natl Acad Sci USA 1992 89 10951 10919
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10951-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
22
-
-
0027361123
-
A structural basis for sequence comparisons. An evaluation of scoring methodologies
-
DOI 10.1006/jmbi.1993.1548
-
A structural basis for sequence comparison. An evaluation of scoring methodologies. MS Johnson, JP Overington, J Mol Biol 1993 233 716 738 10.1006/jmbi.1993.1548 8411177 (Pubitemid 23314782)
-
(1993)
Journal of Molecular Biology
, vol.233
, Issue.4
, pp. 716-738
-
-
Johnson, M.S.1
Overington, J.P.2
-
23
-
-
0033835533
-
Structure-derived substitution matrices for alignment of distantly related sequences
-
10.1093/protein/13.8.545 10964983
-
Structure-derived substitution matrices for alignment of distantly related sequences. A Prli FS Domingues, MJ Sippl, Protein Eng 2000 13 545 550 10.1093/protein/13.8.545 10964983
-
(2000)
Protein Eng
, vol.13
, pp. 545-550
-
-
Prli, A.1
Domingues, F.S.2
Sippl, M.J.3
-
24
-
-
0035937260
-
Pairwise sequence alignment below the twilight zone
-
DOI 10.1006/jmbi.2001.4495
-
Pairwise sequence alignment below the twilight zone. JD Blake, FE Cohen, J Mol Biol 2001 307 721 35 10.1006/jmbi.2001.4495 11254392 (Pubitemid 33027687)
-
(2001)
Journal of Molecular Biology
, vol.307
, Issue.2
, pp. 721-735
-
-
Blake, J.D.1
Cohen, F.E.2
-
25
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
DOI 10.1093/nar/26.1.316
-
Touring protein fold space with Dali/FSSP. L Holm, C Sander, Nucleic Acids Res 1998 26 316 319 10.1093/nar/26.1.316 9399863 (Pubitemid 28291549)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.1
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
26
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. IN Shindyalov, PE Bourne, Protein Eng 1998 11 739 747 10.1093/protein/11.9.739 9796821 (Pubitemid 28434482)
-
(1998)
Protein Engineering
, vol.11
, Issue.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
27
-
-
0034573215
-
Protein structure comparison using SAP
-
11084900
-
Protein structure comparison using SAP. WR Taylor, Methods Mol Biol 2000 143 19 32 11084900
-
(2000)
Methods Mol Biol
, vol.143
, pp. 19-32
-
-
Taylor, W.R.1
-
28
-
-
77951197269
-
FlexSnap: Flexible non-sequential protein structure alignment
-
FlexSnap: flexible non-sequential protein structure alignment. S Salem, MJ Zaki, C Bystroff, Algorithms Mol Biol 2010 4 5 12
-
(2010)
Algorithms Mol Biol
, vol.4
, pp. 5-12
-
-
Salem, S.1
Zaki, M.J.2
Bystroff, C.3
-
29
-
-
0034237578
-
Large-scale comparison of protein sequence alignment algorithms with structure alignments
-
DOI 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7
-
Large-scale comparison of protein sequence alignment algorithms with structural alignments. JM Sauder, JW Artur, RL Dunbrack, Proteins 2000 40 6 22 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7 10813826 (Pubitemid 30368577)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.1
, pp. 6-22
-
-
Sauder, J.M.1
Arthur, J.W.2
Dunbrack Jr., R.L.3
-
30
-
-
0036145804
-
A comparison of position-specific score matrices based on sequence and structure alignments
-
DOI 10.1110/ps.19902
-
A comparison of position-specific score matrices based on sequence and structure alignments. AR Panchenko, SH Bryant, Prot Sci 2002 11 361 370 (Pubitemid 34075799)
-
(2002)
Protein Science
, vol.11
, Issue.2
, pp. 361-370
-
-
Panchenko, A.R.1
Bryant, S.H.2
-
31
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
HOMSTRAD: a database of protein structure alignments for homologous families. K Mizuguchi, CM Deane, TL Blundell, JP Overington, Protein Sci 1998 7 2469 2471 10.1002/pro.5560071126 9828015 (Pubitemid 28506965)
-
(1998)
Protein Science
, vol.7
, Issue.11
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Overington, J.P.4
-
32
-
-
2942517966
-
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
-
DOI 10.1186/1471-2105-4-47
-
OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. GP Raghava, SM Searle, PC Audley, JD Barber, GJ Barton, BMC Bioinformatics 2003 4 47 10.1186/1471-2105-4-47 14552658 (Pubitemid 38751223)
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 47
-
-
Raghava, G.P.S.1
Searle, S.M.J.2
Audley, P.C.3
Barber, J.D.4
Barton, G.J.5
-
33
-
-
16344394781
-
SABmark - A benchmark for sequence alignment that covers the entire known fold space
-
DOI 10.1093/bioinformatics/bth493
-
SABmark-a benchmark for sequence alignment that covers the entire known fold space. I Van Walle, I Lasters, L Wyns, Bioinformatics 2005 21 1267 1268 10.1093/bioinformatics/bth493 15333456 (Pubitemid 40467955)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1267-1268
-
-
Van Walle, I.1
Lasters, I.2
Wyns, L.3
-
34
-
-
2342420462
-
Fold-specific substitution matrices for protein classification
-
DOI 10.1093/bioinformatics/btg492
-
Fold-specific substitution matrices for protein classification. RB Vilim, RM Cunningham, B Lu, P Kheradpour, FJ Stevens, Bioinformatics 2004 20 847 853 10.1093/bioinformatics/btg492 14764567 (Pubitemid 38559724)
-
(2004)
Bioinformatics
, vol.20
, Issue.6
, pp. 847-853
-
-
Vilim, R.B.1
Cunningham, R.M.2
Lu, B.3
Kheradpour, P.4
Stevens, F.J.5
-
35
-
-
78449276763
-
Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices
-
21071807
-
Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices. A Agrawal, X Huang, IEEE/ACM Trans Comput Biol Bioinform 2011 8 194 205 21071807
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, pp. 194-205
-
-
Agrawal, A.1
Huang, X.2
-
36
-
-
0033977962
-
SCOP: A structural classification of proteins database
-
SCOP: a structural classification of proteins database. L Lo Conte, B Ailey, TJ Hubbard, SE Brenner, AG Murzin, C Chothia, Nucleic Acids Res 2000 28 257 259 10.1093/nar/28.1.257 10592240 (Pubitemid 30047773)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 257-259
-
-
Lo Conte, L.1
Ailey, B.2
Hubbard, T.J.P.3
Brenner, S.E.4
Murzin, A.G.5
Chothia, C.6
-
37
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Twilight zone of protein sequence alignments. B Rost, Protein Eng 1999 12 85 94 10.1093/protein/12.2.85 10195279 (Pubitemid 29103686)
-
(1999)
Protein Engineering
, vol.12
, Issue.2
, pp. 85-94
-
-
Rost, B.1
-
38
-
-
0036134748
-
Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
-
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. T Müller, R Spang, M Vingron, Mol Biol Evol 2002 19 8 13 11752185 (Pubitemid 34008042)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.1
, pp. 8-13
-
-
Muller, T.1
Spang, R.2
Vingron, M.3
-
39
-
-
0036721466
-
Optimization of a new score function for the generation of accurate alignments
-
DOI 10.1002/prot.10132
-
Optimization of a new score function for the generation of accurate alignments. B Qian, RA Goldstein, Proteins 2002 48 605 610 10.1002/prot.10132 12211027 (Pubitemid 34925448)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, Issue.4
, pp. 605-610
-
-
Qian, B.1
Goldstein, R.A.2
-
40
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
10.1126/science.1604319 1604319
-
Exhaustive matching of the entire protein sequence database. GH Gonnet, MA Cohen, SA Benner, Science 1992 256 1443 1445 10.1126/science.1604319 1604319
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
|