-
1
-
-
0032831070
-
Structural genomics: Beyond the human genome project
-
SK Burley SC Almo JB Bonanno M Capel MR Chance T Gaasterland D Lin A Sali FW Studier S Swaminathan 1999 Structural genomics: beyond the human genome project Nat Genet 23 151
-
(1999)
Nat Genet
, vol.23
, pp. 151
-
-
Burley, S.K.1
Almo, S.C.2
Bonanno, J.B.3
Capel, M.4
Chance, M.R.5
Gaasterland, T.6
Lin, D.7
Sali, A.8
Studier, F.W.9
Swaminathan, S.10
-
3
-
-
0028849881
-
Homology modeling by the ICM method
-
10.1002/prot.340230314
-
T Cardozo M Totrov R Abagyan 1995 Homology modeling by the ICM method Proteins 23 403 10.1002/prot.340230314
-
(1995)
Proteins
, vol.23
, pp. 403
-
-
Cardozo, T.1
Totrov, M.2
Abagyan, R.3
-
5
-
-
33645734536
-
Protein structure modeling in the proteomics era
-
10.1586/14789450.1.1.97
-
A Fiser 2004 Protein structure modeling in the proteomics era Expert Rev Proteomics 1 97 110 10.1586/14789450.1.1.97
-
(2004)
Expert Rev Proteomics
, vol.1
, pp. 97-110
-
-
Fiser, A.1
-
6
-
-
0019888748
-
Comparative model-building of the mammalian serine proteases
-
10.1016/0022-2836(81)90465-4
-
J Greer 1981 Comparative model-building of the mammalian serine proteases J Mol Biol 153 1027 10.1016/0022-2836(81)90465-4
-
(1981)
J Mol Biol
, vol.153
, pp. 1027
-
-
Greer, J.1
-
7
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
10.1016/0022-2836(92)90964-L
-
M Levitt 1992 Accurate modeling of protein conformation by automatic segment matching J Mol Biol 226 507 10.1016/0022-2836(92)90964-L
-
(1992)
J Mol Biol
, vol.226
, pp. 507
-
-
Levitt, M.1
-
8
-
-
0001433241
-
Knowledge based modelling of homologous proteins, part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
-
10.1093/protein/1.5.377
-
MJ Sutcliffe I Haneef D Carney TL Blundell 1987 Knowledge based modelling of homologous proteins, part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures Protein Eng 1 377 10.1093/protein/1.5.377
-
(1987)
Protein Eng
, vol.1
, pp. 377
-
-
Sutcliffe, M.J.1
Haneef, I.2
Carney, D.3
Blundell, T.L.4
-
9
-
-
0032606105
-
Sequence to structure alignment in comparative modeling using PrISM
-
doi:10.1002/(SICI)1097-0134(1999)37:3+<66::AID-PROT10>3.0.CO;2-K
-
AS Yang B Honig 1999 Sequence to structure alignment in comparative modeling using PrISM Proteins 37 66 doi:10.1002/(SICI)1097-0134(1999)37: 3+<66::AID-PROT10>3.0.CO;2-K
-
(1999)
Proteins
, vol.37
, pp. 66
-
-
Yang, A.S.1
Honig, B.2
-
10
-
-
33646075470
-
Multiple mapping method: A novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling
-
10.1002/prot.20835
-
BK Rai A Fiser 2006 Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling Proteins Struct Funct Bioinform 63 644 661 10.1002/prot.20835
-
(2006)
Proteins Struct Funct Bioinform
, vol.63
, pp. 644-661
-
-
Rai, B.K.1
Fiser, A.2
-
11
-
-
33750414092
-
MMM: A sequence-to-structure alignment protocol
-
10.1093/bioinformatics/btl449
-
BK Rai CJ Madrid-Aliste JE Fajardo A Fiser 2006 MMM: a sequence-to-structure alignment protocol Bioinformatics 22 2691 2692 10.1093/bioinformatics/btl449
-
(2006)
Bioinformatics
, vol.22
, pp. 2691-2692
-
-
Rai, B.K.1
Madrid-Aliste, C.J.2
Fajardo, J.E.3
Fiser, A.4
-
12
-
-
0031307019
-
Evaluation of comparative protein structure modeling by MODELLER-3
-
doi:10.1002/(SICI)1097-0134(1997)1+<50::AID-PROT8>3.0.CO;2-S
-
Sanchez R, Sali A (1997) Evaluation of comparative protein structure modeling by MODELLER-3. Proteins (Suppl 1):50-58. doi:10.1002/(SICI)1097- 0134(1997)1+<50::AID-PROT8>3.0.CO;2-S
-
(1997)
Proteins (Suppl 1)
, pp. 50-58
-
-
Sanchez, R.1
Sali, A.2
-
13
-
-
30344454371
-
Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment
-
Suppl 7. 10.1002/prot.20725
-
C Venclovas M Margelevicius 2005 Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment Proteins 61 Suppl 7 99 105 10.1002/prot.20725
-
(2005)
Proteins
, vol.61
, pp. 99-105
-
-
Venclovas, C.1
Margelevicius, M.2
-
14
-
-
0242299188
-
Novel use of a genetic algorithm for protein structure prediction: Searching template and sequence alignment space
-
Suppl 6. 10.1002/prot.10549
-
B Contreras-Moreira PW Fitzjohn M Offman GR Smith PA Bates 2003 Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space Proteins 53 Suppl 6 424 429 10.1002/prot.10549
-
(2003)
Proteins
, vol.53
, pp. 424-429
-
-
Contreras-Moreira, B.1
Fitzjohn, P.W.2
Offman, M.3
Smith, G.R.4
Bates, P.A.5
-
16
-
-
35748965848
-
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
-
10.1093/bioinformatics/btm377
-
N Fernandez-Fuentes BK Rai CJ Madrid-Aliste J Eduardo Fajardo A Fiser 2007 Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments Bioinformatics 23 2558 2565 10.1093/bioinformatics/btm377
-
(2007)
Bioinformatics
, vol.23
, pp. 2558-2565
-
-
Fernandez-Fuentes, N.1
Rai, B.K.2
Madrid-Aliste, C.J.3
Eduardo Fajardo, J.4
Fiser, A.5
-
17
-
-
0033954256
-
The Protein Data Bank
-
10.1093/nar/28.1.235
-
HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The Protein Data Bank Nucleic Acids Res 28 235 10.1093/nar/28.1.235
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
18
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
10.1093/bioinformatics/btl158
-
W Li A Godzik 2006 Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 1658 10.1093/bioinformatics/btl158
-
(2006)
Bioinformatics
, vol.22
, pp. 1658
-
-
Li, W.1
Godzik, A.2
-
19
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
10.1093/nar/22.22.4673
-
JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680 10.1093/nar/22.22.4673
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
21
-
-
0032506030
-
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome
-
10.1073/pnas.95.23.13597
-
R Sanchez A Sali 1998 Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc Natl Acad Sci USA 95 13597 13602 10.1073/pnas.95.23.13597
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 13597-13602
-
-
Sanchez, R.1
Sali, A.2
-
22
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340
-
RC Edgar 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 32 1792 1797 10.1093/nar/gkh340
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
23
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
-
10.1002/prot.340140216
-
RB Russell GJ Barton 1992 Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels Proteins 14 309 323 10.1002/prot.340140216
-
(1992)
Proteins
, vol.14
, pp. 309-323
-
-
Russell, R.B.1
Barton, G.J.2
-
24
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
10.1006/jmbi.2001.4762
-
J Shi TL Blundell K Mizuguchi 2001 FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties J Mol Biol 310 243 10.1006/jmbi.2001.4762
-
(2001)
J Mol Biol
, vol.310
, pp. 243
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
25
-
-
0031564630
-
A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
-
10.1006/jmbi.1997.0924
-
DW Rice D Eisenberg 1997 A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence J Mol Biol 267 1026 1038 10.1006/jmbi.1997.0924
-
(1997)
J Mol Biol
, vol.267
, pp. 1026-1038
-
-
Rice, D.W.1
Eisenberg, D.2
-
26
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
10.1006/jmbi.1996.0114
-
S Miyazawa RL Jernigan 1996 Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading J Mol Biol 256 623 644 10.1006/jmbi.1996.0114
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
27
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
10.1073/pnas.89.22.10915
-
S Henikoff JG Henikoff 1992 Amino acid substitution matrices from protein blocks Proc Natl Acad Sci USA 89 10915 10919 10.1073/pnas.89.22.10915
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
28
-
-
34247281977
-
Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials
-
10.1002/prot.21279
-
D Rykunov A Fiser 2007 Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials Proteins Struct Funct Bioinform 67 559 568 10.1002/prot.21279
-
(2007)
Proteins Struct Funct Bioinform
, vol.67
, pp. 559-568
-
-
Rykunov, D.1
Fiser, A.2
|