-
1
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl MJ: Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995, 5(2):229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, Issue.2
, pp. 229-235
-
-
Sippl, M.J.1
-
2
-
-
0030596063
-
How to derive a protein folding potential? A new approach to an old problem
-
Mirny L, Shakhnovich E: How to derive a protein folding potential?A new approach to an old problem. J Mol Biol 1996, 264(5):1164-1179.
-
(1996)
J Mol Biol
, vol.264
, Issue.5
, pp. 1164-1179
-
-
Mirny, L.1
Shakhnovich, E.2
-
3
-
-
0033566614
-
An empirical energy potential with a reference state for protein fold and sequence recognition
-
Miyazawa S, Jernigan R: An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999, 36(3):357-369.
-
(1999)
Proteins
, vol.36
, Issue.3
, pp. 357-369
-
-
Miyazawa, S.1
Jernigan, R.2
-
4
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M: Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000, 10(2):139-145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, Issue.2
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
5
-
-
0347417009
-
Optimizing physical energy functions for protein folding
-
Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG: Optimizing physical energy functions for protein folding. Proteins 2004, 54(1):88-103.
-
(2004)
Proteins
, vol.54
, Issue.1
, pp. 88-103
-
-
Fujitsuka, Y.1
Takada, S.2
Luthey-Schulten, Z.A.3
Wolynes, P.G.4
-
6
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
Stote R, Straub J, Watanabe M, Wiorkiewicz Kuczera J, Yin D, Karplus M: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem 1998, 102(18):3586-3617.
-
(1998)
J Phys Chem
, vol.102
, Issue.18
, pp. 3586-3617
-
-
Stote, R.1
Straub, J.2
Watanabe, M.3
Wiorkiewicz Kuczera, J.4
Yin, D.5
Karplus, M.6
-
7
-
-
0000837770
-
Directional Hydrogen Bonding in the MM3 Force Field. II
-
Lii JH, Allinger NL: Directional Hydrogen Bonding in the MM3 Force Field. II. J Comp Chem 1998, 19(9):1001-1016.
-
(1998)
J Comp Chem
, vol.19
, Issue.9
, pp. 1001-1016
-
-
Lii, J.H.1
Allinger, N.L.2
-
8
-
-
19544362526
-
Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions
-
Fang Q, Shortle D: Enhanced sampling near the native conformation using statistical potentials for local side-chain and backbone interactions. Proteins 2005, 60(1):97-102.
-
(2005)
Proteins
, vol.60
, Issue.1
, pp. 97-102
-
-
Fang, Q.1
Shortle, D.2
-
9
-
-
19544371352
-
A consistent set of statistical potentials for quantifying local side-chain and backbone interactions
-
Fang Q, Shortle D: A consistent set of statistical potentials for quantifying local side-chain and backbone interactions. Proteins 2005, 60(1):90-96.
-
(2005)
Proteins
, vol.60
, Issue.1
, pp. 90-96
-
-
Fang, Q.1
Shortle, D.2
-
10
-
-
0346458791
-
A new pairwise folding potential based on improved decoy generation and side-chain packing
-
Loose C, Klepeis JL, Floudas CA: A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins 2004, 54(2):303-314.
-
(2004)
Proteins
, vol.54
, Issue.2
, pp. 303-314
-
-
Loose, C.1
Klepeis, J.L.2
Floudas, C.A.3
-
11
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo F, Sanchez R, Sali A: Statistical potentials for fold assessment. Protein Sci 2002, 11(2):430-448.
-
(2002)
Protein Sci
, vol.11
, Issue.2
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
12
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman P: Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998, 282(5389):740-744.
-
(1998)
Science
, vol.282
, Issue.5389
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.2
-
13
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luthy R, Eisenberg DA: a method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253(5016):164-170.
-
(1991)
Science
, vol.253
, Issue.5016
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.A.3
-
14
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang E, Baker D: Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997, 268(1):209-225.
-
(1997)
J Mol Biol
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
15
-
-
0242267517
-
Critical Assessment of methods of protein structure prediction (CASP) - Round V
-
Moult J, Fidelis K, Zemla A, Hubbard T: Critical Assessment of methods of protein structure prediction (CASP) - Round V. Proteins 2003, 53(Suppl 6):334-339.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 334-339
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
Hubbard, T.4
-
16
-
-
0032540222
-
Assessing protein structures with a non-local atomic interaction energy
-
Melo F, Feytmans E: Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 1998, 277(5):1141-1152.
-
(1998)
J Mol Biol
, vol.277
, Issue.5
, pp. 1141-1152
-
-
Melo, F.1
Feytmans, E.2
-
17
-
-
0035255016
-
Identification and ab initio simulations of early folding units in proteins
-
Gilis D, Rooman M: Identification and ab initio simulations of early folding units in proteins. Proteins 2001, 42(2):164-176.
-
(2001)
Proteins
, vol.42
, Issue.2
, pp. 164-176
-
-
Gilis, D.1
Rooman, M.2
-
18
-
-
2542631929
-
Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
-
Zhou H, Zhou Y: Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004, 55(4):1005-1013.
-
(2004)
Proteins
, vol.55
, Issue.4
, pp. 1005-1013
-
-
Zhou, H.1
Zhou, Y.2
-
19
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ: Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990, 213(4):859-883.
-
(1990)
J Mol Biol
, vol.213
, Issue.4
, pp. 859-883
-
-
Sippl, M.J.1
-
20
-
-
0027650879
-
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
-
Sippl MJ: Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 1993, 7(4):473-501.
-
(1993)
J Comput Aided Mol Des
, vol.7
, Issue.4
, pp. 473-501
-
-
Sippl, M.J.1
-
21
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J: An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998, 275(5):895-916.
-
(1998)
J Mol Biol
, vol.275
, Issue.5
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
22
-
-
0031582083
-
Novel knowledge-based mean force potential at atomic level
-
Melo F, Feytmans E: Novel knowledge-based mean force potential at atomic level. J Mol Biol 1997, 267(1):207-222.
-
(1997)
J Mol Biol
, vol.267
, Issue.1
, pp. 207-222
-
-
Melo, F.1
Feytmans, E.2
-
23
-
-
24644464131
-
An atomic environment potential for use in protein structure prediction
-
Summa CM, Levitt M, Degrado WF: An atomic environment potential for use in protein structure prediction. J Mol Biol 2005, 352(4):986-1001.
-
(2005)
J Mol Biol
, vol.352
, Issue.4
, pp. 986-1001
-
-
Summa, C.M.1
Levitt, M.2
Degrado, W.F.3
-
24
-
-
24344479166
-
Atomically detailed potentials to recognize native and approximate protein structures
-
Qiu J, Elber R: Atomically detailed potentials to recognize native and approximate protein structures. Proteins 2005, 61(1):44-55.
-
(2005)
Proteins
, vol.61
, Issue.1
, pp. 44-55
-
-
Qiu, J.1
Elber, R.2
-
25
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J: A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001, 44(3):223-232.
-
(2001)
Proteins
, vol.44
, Issue.3
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
26
-
-
0642340510
-
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
-
Berrera M, Molinari H, Fogolari F: Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 2003, 4:8.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 8
-
-
Berrera, M.1
Molinari, H.2
Fogolari, F.3
-
27
-
-
0030310296
-
Fast protein fold recognition via sequence to structure alignment and capacity
-
London, UK
-
Alexandrov NN, Nussinov R, Zimmer RM: Fast protein fold recognition via sequence to structure alignment and capacity: London, UK.; 1996:53-72.
-
(1996)
, pp. 53-72
-
-
Alexandrov, N.N.1
Nussinov, R.2
Zimmer, R.M.3
-
28
-
-
0033537993
-
GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
-
Jones DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287(4):797-815.
-
(1999)
J Mol Biol
, vol.287
, Issue.4
, pp. 797-815
-
-
Jones, D.T.1
-
29
-
-
0030767485
-
VERIFY3D: Assessment of protein models with three-dimensional profiles
-
Eisenberg D, Luthy R, Bowie JU: VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997, 277:396-404.
-
(1997)
Methods Enzymol
, vol.277
, pp. 396-404
-
-
Eisenberg, D.1
Luthy, R.2
Bowie, J.U.3
-
30
-
-
25444513982
-
Clustering the annotation space of proteins
-
A. OC:
-
Kunin V, A. OC: Clustering the annotation space of proteins. BMC Bioinformatics 2005, 6:24.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 24
-
-
Kunin, V.1
-
31
-
-
11844265970
-
Protein sequence randomization: Efficient estimation of protein stability using knowledge-based potentials
-
Wiederstein M, Sippl MJ: Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. J Mol Biol 2005, 345(5):1199-1212.
-
(2005)
J Mol Biol
, vol.345
, Issue.5
, pp. 1199-1212
-
-
Wiederstein, M.1
Sippl, M.J.2
-
32
-
-
0034333083
-
How to generate improved potentials for protein tertiary structure prediction: A lattice model study
-
Chiu TL, Goldstein RA: How to generate improved potentials for protein tertiary structure prediction: a lattice model study. Proteins 2000, 41(2):157-163.
-
(2000)
Proteins
, vol.41
, Issue.2
, pp. 157-163
-
-
Chiu, T.L.1
Goldstein, R.A.2
-
33
-
-
0347130904
-
Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment
-
Yang WY, Pitera JW, Swope WC, Gruebele M: Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment. J Mol Biol 2004, 336(1):241-251.
-
(2004)
J Mol Biol
, vol.336
, Issue.1
, pp. 241-251
-
-
Yang, W.Y.1
Pitera, J.W.2
Swope, W.C.3
Gruebele, M.4
-
34
-
-
33144460796
-
Local protein structure prediction using discriminative models
-
Sander O, Sommer I, Lengauer T: Local protein structure prediction using discriminative models. BMC Bioinformatics 2006, 7:14.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 14
-
-
Sander, O.1
Sommer, I.2
Lengauer, T.3
-
35
-
-
0030801002
-
Gapped Blast and Psi-blast: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped Blast and Psi-blast: a new generation of protein database search programs. Nucleic Acids Research 1997, 25(17):3389-3402.
-
(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.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
36
-
-
25444459890
-
Windows.NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)
-
Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR: Windows.NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST). BMC Bioinformatics 2005, 6:93.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 93
-
-
Dowd, S.E.1
Zaragoza, J.2
Rodriguez, J.R.3
Oliver, M.J.4
Payton, P.R.5
-
37
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D: An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003, 53(1):76-87.
-
(2003)
Proteins
, vol.53
, Issue.1
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Morozov, A.V.3
Kuhlman, B.4
Rohl, C.A.5
Baker, D.6
-
38
-
-
24344503448
-
PROSTAR: The protein potential test site
-
Braxenthaler M, Samudrala R, Pedersen J, Luo R, Milash B, Moult J: PROSTAR: The protein potential test site. [http://prostar.carb.nist.gov].
-
-
-
Braxenthaler, M.1
Samudrala, R.2
Pedersen, J.3
Luo, R.4
Milash, B.5
Moult, J.6
-
39
-
-
0026505184
-
Evaluation of protein models by atomic solvation preference
-
Holm L, Sander C: Evaluation of protein models by atomic solvation preference. J Mol Biol 1992, 225(1):93-105.
-
(1992)
J Mol Biol
, vol.225
, Issue.1
, pp. 93-105
-
-
Holm, L.1
Sander, C.2
-
40
-
-
0031556019
-
Folding simulation with genetic algorithms and a detailed molecular description
-
Pedersen JT, Moult J: Folding simulation with genetic algorithms and a detailed molecular description. J Mol Biol 1997, 269(2):240-259.
-
(1997)
J Mol Biol
, vol.269
, Issue.2
, pp. 240-259
-
-
Pedersen, J.T.1
Moult, J.2
-
41
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
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
-
42
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
Zhang C, Liu S, Zhou H, Zhou Y: An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004, 13(2):400-411.
-
(2004)
Protein Sci
, vol.13
, Issue.2
, pp. 400-411
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
43
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
-
Park B, Levitt M: Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996, 258(2):367-392.
-
(1996)
J Mol Biol
, vol.258
, Issue.2
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
44
-
-
0038708222
-
A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics
-
Keasar C, Levitt M: A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol 2003, 329(1):159-174.
-
(2003)
J Mol Biol
, vol.329
, Issue.1
, pp. 159-174
-
-
Keasar, C.1
Levitt, M.2
-
45
-
-
0032612579
-
Ab initio protein structure prediction of CASP III targets using ROSETTA
-
Simons KT, Bonneau R, Ruczinski I, Baker D: Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins 1999, 37(Suppl 3):171-176.
-
(1999)
Proteins
, vol.37
, Issue.SUPPL. 3
, pp. 171-176
-
-
Simons, K.T.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
46
-
-
0032611514
-
A combined approach for ab initio construction of low resolution protein tertiary structures from sequence
-
Samudrala R, Xia Y, Levitt M, Huang ES: A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac Symp Biocomput 1999:505-516.
-
(1999)
Pac Symp Biocomput
, pp. 505-516
-
-
Samudrala, R.1
Xia, Y.2
Levitt, M.3
Huang, E.S.4
-
47
-
-
4544355522
-
Improved protein structure selection using decoy-dependent discriminatory functions
-
Wang K, Fain B, Levitt M, Samudrala R: Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol 2004, 4(1):8.
-
(2004)
BMC Struct Biol
, vol.4
, Issue.1
, pp. 8
-
-
Wang, K.1
Fain, B.2
Levitt, M.3
Samudrala, R.4
-
48
-
-
13444266488
-
A simple and fast secondary structure prediction method using hidden neural networks
-
Lin K, Simossis VA, Taylor WR, Heringa J: A simple and fast secondary structure prediction method using hidden neural networks. BioInformatics 2005, 21(2):152-159.
-
(2005)
BioInformatics
, vol.21
, Issue.2
, pp. 152-159
-
-
Lin, K.1
Simossis, V.A.2
Taylor, W.R.3
Heringa, J.4
-
49
-
-
32644441676
-
Prediction of protein structural class with Rough Sets
-
Cao Y, Liu S, Zhang L, Qin J, Wang J, Tang K: Prediction of protein structural class with Rough Sets. BMC Bioinformatics 2006, 7:20.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 20
-
-
Cao, Y.1
Liu, S.2
Zhang, L.3
Qin, J.4
Wang, J.5
Tang, K.6
-
50
-
-
20844438512
-
Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues
-
Anand B, Gowri VS, Srinivasan N: Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues. Bioinformatics 2005, 21(12):2821-2826.
-
(2005)
Bioinformatics
, vol.21
, Issue.12
, pp. 2821-2826
-
-
Anand, B.1
Gowri, V.S.2
Srinivasan, N.3
-
51
-
-
33644843469
-
On single and multiple models of protein families for the detection of remote sequence relationships
-
Casbon JA, Saqi MA: On single and multiple models of protein families for the detection of remote sequence relationships. BMC Bioinformatics 2006, 7:48.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 48
-
-
Casbon, J.A.1
Saqi, M.A.2
-
52
-
-
27544437865
-
A hybrid machine-learning approach for segmentation of protein localization data
-
Kasson PM, Huppa JB, Davis MM, Brunger AT: A hybrid machine-learning approach for segmentation of protein localization data. Bioinformatics 2005, 21(19):3778-3786.
-
(2005)
Bioinformatics
, vol.21
, Issue.19
, pp. 3778-3786
-
-
Kasson, P.M.1
Huppa, J.B.2
Davis, M.M.3
Brunger, A.T.4
-
53
-
-
29244465822
-
An SVM-based system for predicting protein subnuclear localizations
-
Lei Z, Dai Y: An SVM-based system for predicting protein subnuclear localizations. BMC Bioinformatics 2005, 6:291.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 291
-
-
Lei, Z.1
Dai, Y.2
-
54
-
-
17844363963
-
PPRODO: Prediction of protein domain boundaries using neural networks
-
Sim J, Kim SY, Lee J: PPRODO: prediction of protein domain boundaries using neural networks. Proteins 2005, 59(3):627-632.
-
(2005)
Proteins
, vol.59
, Issue.3
, pp. 627-632
-
-
Sim, J.1
Kim, S.Y.2
Lee, J.3
-
55
-
-
11344292852
-
Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments
-
Zhou H, Zhou Y: Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 2005, 58(2):321-328.
-
(2005)
Proteins
, vol.58
, Issue.2
, pp. 321-328
-
-
Zhou, H.1
Zhou, Y.2
-
56
-
-
10844235653
-
Optimal docking area: A new method for predicting protein-protein interaction sites
-
Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R: Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005, 58(1):134-143.
-
(2005)
Proteins
, vol.58
, Issue.1
, pp. 134-143
-
-
Fernandez-Recio, J.1
Totrov, M.2
Skorodumov, C.3
Abagyan, R.4
-
57
-
-
25444527443
-
Improved prediction of critical residues for protein function based on network and phylogenetic analyses
-
Thibert B, Bredesen DE, Del Rio G: Improved prediction of critical residues for protein function based on network and phylogenetic analyses. BMC Bioinformatics 2005, 6(1):213.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.1
, pp. 213
-
-
Thibert, B.1
Bredesen, D.E.2
Del Rio, G.3
-
58
-
-
0041886960
-
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
-
Mittelman D, Sadreyev R, Grishin N: Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics 2003, 19(12):1531-1539.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1531-1539
-
-
Mittelman, D.1
Sadreyev, R.2
Grishin, N.3
-
59
-
-
4444298729
-
Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods
-
Ohlson T, Wallner B, Elofsson A: Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 2004, 57(1):188-197.
-
(2004)
Proteins
, vol.57
, Issue.1
, pp. 188-197
-
-
Ohlson, T.1
Wallner, B.2
Elofsson, A.3
-
60
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
Mizuguchi K, Deane CM, Blundell TL, Overington JP: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci 1998, 7(11):2469-2471.
-
(1998)
Protein Sci
, vol.7
, Issue.11
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Overington, J.P.4
-
61
-
-
29244479220
-
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
-
Fogolari F, Tosatto SC, Colombo G: A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics 2005, 6:301.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 301
-
-
Fogolari, F.1
Tosatto, S.C.2
Colombo, G.3
-
62
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779-815.
-
(1993)
J Mol Biol
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
63
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
(database issue)
-
Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzi AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Research 2004, 32(database issue):D226-D229.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.P.4
Chothia, C.5
Murzi, A.G.6
-
64
-
-
0348129526
-
The ASTRAL Compendium in 2004
-
(database issue)
-
Chandonia JM, Hon G, Walker NS, Conte LL, Koehl P, Levitt M, Brenner SE: The ASTRAL Compendium in 2004. Nucleic acids research 2004, 32(database issue): 189-192.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 189-192
-
-
Chandonia, J.M.1
Hon, G.2
Walker, N.S.3
Conte, L.L.4
Koehl, P.5
Levitt, M.6
Brenner, S.E.7
-
65
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RLJ: PISCES: a protein sequence culling server. Bioinformatics 2003, 19(12):1589-1591.
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack, R.L.J.2
-
66
-
-
0031829372
-
Removing near-neighbour redundancy from large protein sequence collections
-
Holm L, Sander C: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 1998, 14(5):423-429.
-
(1998)
Bioinformatics
, vol.14
, Issue.5
, pp. 423-429
-
-
Holm, L.1
Sander, C.2
-
67
-
-
0028043552
-
Position-based sequence weights
-
Henikoff S, Henikoff JG: Position-based sequence weights. J Mol Biol 1994, 243(4):574-578.
-
(1994)
J Mol Biol
, vol.243
, Issue.4
, pp. 574-578
-
-
Henikoff, S.1
Henikoff, J.G.2
-
68
-
-
0023042012
-
Information content of binding sites on nucleotide sequences
-
Schneider TS, Stormo GD, Gold L, Ehrenfeucht A: Information content of binding sites on nucleotide sequences. J Mol Biol 1986, 188(3):415-431.
-
(1986)
J Mol Biol
, vol.188
, Issue.3
, pp. 415-431
-
-
Schneider, T.S.1
Stormo, G.D.2
Gold, L.3
Ehrenfeucht, A.4
-
69
-
-
0028091659
-
Detection of conserved segments in proteins: Iterative scanning of sequence databases with alignment blocks
-
Tatusov RL, Altschul SF, Koonin EV: Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc Natl Acad Sci USA 1994, 91(25):12091-12095.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, Issue.25
, pp. 12091-12095
-
-
Tatusov, R.L.1
Altschul, S.F.2
Koonin, E.V.3
-
70
-
-
0027903113
-
-
Menlo Park, CA. AAAI Press
-
Brown M, Hughey R, Krogh A, Mian IS, Sjölander K, Haussler D: Dirichlet Mixture priors to derive hidden Markov models for protein families: Menlo Park, CA. AAAI Press; 1993:47-55.
-
(1993)
Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families
, pp. 47-55
-
-
Brown, M.1
Hughey, R.2
Krogh, A.3
Mian, I.S.4
Sjölander, K.5
Haussler, D.6
|