-
1
-
-
32144432437
-
The SWISS-MODEL Work-space: a web-based environment for protein structure homology modelling
-
10.1093/bioinformatics/bti770, 16301204
-
Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL Work-space: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22:195-201. 10.1093/bioinformatics/bti770, 16301204.
-
(2006)
Bioinformatics
, vol.22
, pp. 195-201
-
-
Arnold, K.1
Bordoli, L.2
Kopp, J.3
Schwede, T.4
-
2
-
-
20844462588
-
MolIDE: a homology modeling framework you can click with
-
10.1093/bioinformatics/bti438, 15845657
-
Canutescu AA, Dunbrack RL. MolIDE: a homology modeling framework you can click with. Bioinformatics 2005, 21:2914-2916. 10.1093/bioinformatics/bti438, 15845657.
-
(2005)
Bioinformatics
, vol.21
, pp. 2914-2916
-
-
Canutescu, A.A.1
Dunbrack, R.L.2
-
3
-
-
4444221565
-
UCSF Chimera--a visualization system for exploratory re-search and analysis
-
10.1002/jcc.20084, 15264254
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory re-search and analysis. J Comput Chem 2004, 25:1605-1612. 10.1002/jcc.20084, 15264254.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
4
-
-
63849246525
-
Protein structure prediction on the web: a case study using the Phyre server
-
Kelley LA, Sternberg MJE. Protein structure prediction on the web: a case study using the Phyre server. Nature Protocols 2009, 4:363-371.
-
(2009)
Nature Protocols
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
5
-
-
77954293798
-
CPHmodels-3.0 - Remote homology modeling using structure guided sequence profiles
-
10.1093/nar/gkq535, 2896139, 20542909
-
Nielsen M, Lundegaard C, Lund O, Petersen TN. CPHmodels-3.0 - Remote homology modeling using structure guided sequence profiles. Nucleic Acids Research 2010, 38:W576-W581. 10.1093/nar/gkq535, 2896139, 20542909.
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Nielsen, M.1
Lundegaard, C.2
Lund, O.3
Petersen, T.N.4
-
6
-
-
0003845223
-
The PyMOL Molecular Graphics System
-
San Carlos, CA: DeLano Scientific
-
DeLano WL. The PyMOL Molecular Graphics System. 2002, San Carlos, CA: DeLano Scientific.
-
(2002)
-
-
DeLano, W.L.1
-
7
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
8
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
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, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
9
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340, 390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
10
-
-
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, 308517, 7984417
-
Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
11
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 9:739-747.
-
(1998)
Protein Eng
, vol.9
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
12
-
-
43749107283
-
Comparative protein structure modeling using MODELLER
-
Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 2006, Chapter 5:Unit 5.6.
-
(2006)
Curr Protoc Bioinformatics
, vol.Chapter 5
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.Y.6
Pieper, U.7
Sali, A.8
-
13
-
-
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
-
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 1970, 48:443-453. 10.1016/0022-2836(70)90057-4, 5420325.
-
(1970)
Journal of Molecular Biology
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
14
-
-
0019887799
-
Identification of common molecular subsequences
-
10.1016/0022-2836(81)90087-5, 7265238
-
Smith TF, Waterman MS. Identification of common molecular subsequences. Journal of Molecular Biology 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
-
(1981)
Journal of Molecular Biology
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
15
-
-
67849103758
-
HHomp--prediction and classification of outer membrane proteins
-
10.1093/nar/gkp325, 2703889, 19429691
-
Remmert M, Linke D, Lupas AN, Soding J. HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res 2009, 37:W446-W451. 10.1093/nar/gkp325, 2703889, 19429691.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Remmert, M.1
Linke, D.2
Lupas, A.N.3
Soding, J.4
-
16
-
-
0036307493
-
Within the Twilight Zone: a sensitive profile-profile comparison tool based on information theory
-
10.1006/jmbi.2001.5293, 11827492
-
Yona G, Levitt M. Within the Twilight Zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002, 315:1257-1275. 10.1006/jmbi.2001.5293, 11827492.
-
(2002)
J Mol Biol
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
-
17
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
10.1006/jmbi.2000.4042, 10964570
-
Notredame C, Higgins D, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 2000, 302:205-217. 10.1006/jmbi.2000.4042, 10964570.
-
(2000)
Journal of Molecular Biology
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.2
Heringa, J.3
-
18
-
-
2942619012
-
3DCoffee: combining protein sequences and structures within multiple sequence alignments
-
10.1016/j.jmb.2004.04.058, 15201059
-
O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 2004, 340:385-395. 10.1016/j.jmb.2004.04.058, 15201059.
-
(2004)
J Mol Biol
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
19
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
1160169, 15980461, Web Server issue
-
Söding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33(Web Server issue):W244-W248. 1160169, 15980461.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Söding, J.1
Biegert, A.2
Lupas, A.N.3
-
20
-
-
17744387920
-
All are not equal: a benchmark of different homology modeling programs
-
10.1110/ps.041253405, 2253266, 15840834
-
Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci 2005, 14:1315-27. 10.1110/ps.041253405, 2253266, 15840834.
-
(2005)
Protein Sci
, vol.14
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
-
21
-
-
77956591314
-
EasyModeller: a graphical interface to MODELLER
-
10.1186/1756-0500-3-226, 2936912, 20712861
-
Kuntal BK, Aparoy P, Reddanna P. EasyModeller: a graphical interface to MODELLER. BMC Res Notes 2010, 3:226-330. 10.1186/1756-0500-3-226, 2936912, 20712861.
-
(2010)
BMC Res Notes
, vol.3
, pp. 226-330
-
-
Kuntal, B.K.1
Aparoy, P.2
Reddanna, P.3
-
22
-
-
80255138836
-
SWIFT MODELLER: A JAVA based GUI for molecular modeling
-
10.1007/s00894-011-0960-4, 21258829
-
Mathur A, Shankaracharya, Vidyarthi AS. SWIFT MODELLER: A JAVA based GUI for molecular modeling. J Mol Model 2011, 17:2601-2607. 10.1007/s00894-011-0960-4, 21258829.
-
(2011)
J Mol Model
, vol.17
, pp. 2601-2607
-
-
Mathur, A.1
Shankaracharya2
Vidyarthi, A.S.3
-
23
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
10.1110/ps.062416606, 2242414, 17075131
-
Shen M-Y, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Science 2006, 15:2507-2524. 10.1110/ps.062416606, 2242414, 17075131.
-
(2006)
Protein Science
, vol.15
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
|