-
1
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
2
-
-
0033997036
-
Comparison of sequence profiles. Strategies for structural predictions using sequence information
-
Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
-
(2000)
Protein Sci
, vol.9
, pp. 232-241
-
-
Rychlewski, L.1
Jaroszewski, L.2
Li, W.3
Godzik, A.4
-
3
-
-
33746239564
-
Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences
-
Tan YH, Huang H, Kihara D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins 2006;64:587-600.
-
(2006)
Proteins
, vol.64
, pp. 587-600
-
-
Tan, Y.H.1
Huang, H.2
Kihara, D.3
-
4
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. Profile hidden Markov models. Bioinformatics 1998;14:755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
6
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff MO, editors, Washington, DC: National Biomedical Research Foundation;
-
Dayhoff O, Schwartz RM, Orcutt BC. A model of evolutionary change in proteins. In: Dayhoff MO, editors. Atlas of protein Sequence and Structure. Washington, DC: National Biomedical Research Foundation; 1978. pp 345-352.
-
(1978)
Atlas of protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
7
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 1992;89:10915-10919.
-
(1992)
Proc Natl Acad Sci
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
8
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1433-1445.
-
(1992)
Science
, vol.256
, pp. 1433-1445
-
-
Gonnet, G.H.1
Cohen, M.A.2
Benner, S.A.3
-
9
-
-
0027361123
-
A structural basis for sequence comparisons. An evaluation of scoring methodologies
-
Johnson MS, Overington JP. A structural basis for sequence comparisons. An evaluation of scoring methodologies. J Mol Biol 1993;233:716-738.
-
(1993)
J Mol Biol
, vol.233
, pp. 716-738
-
-
Johnson, M.S.1
Overington, J.P.2
-
10
-
-
0035937260
-
Pairwise sequence alignment below the twilight zone
-
Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol 2001;307:721-735.
-
(2001)
J Mol Biol
, vol.307
, pp. 721-735
-
-
Blake, J.D.1
Cohen, F.E.2
-
11
-
-
0033835533
-
Structure-derived substitution matrices for alignment of distantly related sequences
-
Prlic A, Domingues FS, Sippl MJ. Structure-derived substitution matrices for alignment of distantly related sequences. Protein Eng 2000;13:545-550.
-
(2000)
Protein Eng
, vol.13
, pp. 545-550
-
-
Prlic, A.1
Domingues, F.S.2
Sippl, M.J.3
-
12
-
-
0036721466
-
Optimization of a new score function for the generation of accurate alignments
-
Qian B, Goldstein RA. Optimization of a new score function for the generation of accurate alignments. Proteins 2002;48:605-610.
-
(2002)
Proteins
, vol.48
, pp. 605-610
-
-
Qian, B.1
Goldstein, R.A.2
-
13
-
-
0027057526
-
A database of protein structure families with common folding motifs
-
Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G. A database of protein structure families with common folding motifs. Protein Sci 1992;1:1691-1698.
-
(1992)
Protein Sci
, vol.1
, pp. 1691-1698
-
-
Holm, L.1
Ouzounis, C.2
Sander, C.3
Tuparev, G.4
Vriend, G.5
-
14
-
-
0029115481
-
A sequence property approach to searching protein databases
-
Hobohm U, Sander C. A sequence property approach to searching protein databases. J Mol Biol 1995;251:390-399.
-
(1995)
J Mol Biol
, vol.251
, pp. 390-399
-
-
Hobohm, U.1
Sander, C.2
-
15
-
-
0142184275
-
PROSPECT II: Protein structure prediction program for genome-scale applications
-
Kim D, Xu D, Guo J-t, Ellrott K, Xu Y. PROSPECT II: protein structure prediction program for genome-scale applications. Protein Eng 2003;16:641-650.
-
(2003)
Protein Eng
, vol.16
, pp. 641-650
-
-
Kim, D.1
Xu, D.2
Guo, J.-T.3
Ellrott, K.4
Xu, Y.5
-
16
-
-
0034628922
-
Combination of threading potentials and sequence profiles improves fold recognition
-
Panchenko AR., Marchler-Bauer A, Bryant HJ. Combination of threading potentials and sequence profiles improves fold recognition J Mol Biol 2000;296:1319-1331.
-
(2000)
J Mol Biol
, vol.296
, pp. 1319-1331
-
-
Panchenko, A.R.1
Marchler-Bauer, A.2
Bryant, H.J.3
-
17
-
-
0035967880
-
Fugue: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi J, Blundell TL, Mizuguchi K. Fugue: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001;310:243-257.
-
(2001)
J Mol Biol
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
18
-
-
0034595501
-
Enhanced genome annotation using structural profiles in the program 3D-PSSM
-
Kelly LA, McCallum CM, Stenberg MJ. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000;299:501-522.
-
(2000)
J Mol Biol
, vol.299
, pp. 501-522
-
-
Kelly, L.A.1
McCallum, C.M.2
Stenberg, M.J.3
-
19
-
-
0033654768
-
Hybrid fold recognition: Combining sequence derived properties with evolutionary information
-
Fischer D. Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000;5:119-130.
-
(2000)
Pac Symp Biocomput
, vol.5
, pp. 119-130
-
-
Fischer, D.1
-
20
-
-
0031301955
-
Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds
-
Di Francesco V, Geetha V, Garnier J, Munson PJ. Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds. Proteins 1997; (Suppl 1):123-128.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 123-128
-
-
Di Francesco, V.1
Geetha, V.2
Garnier, J.3
Munson, P.J.4
-
21
-
-
0030310296
-
-
Alexandrov NN, Nussiniv R, Zimmer RM. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. In: Hunter L, Klein T, editors. Biocomputing: Proceedings of the 1996 Pacific Symposium. Singapore: World Scientific Publishing Co. Pac Symp Biocomput 1996;53-72.
-
Alexandrov NN, Nussiniv R, Zimmer RM. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. In: Hunter L, Klein T, editors. Biocomputing: Proceedings of the 1996 Pacific Symposium. Singapore: World Scientific Publishing Co. Pac Symp Biocomput 1996;53-72.
-
-
-
-
22
-
-
0029186289
-
TOPITS: Threading one-dimensional predictions into three-dimensional structures
-
Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structures. ISMB 1995;3:314-321.
-
(1995)
ISMB
, vol.3
, pp. 314-321
-
-
Rost, B.1
-
23
-
-
0027318317
-
An empirical energy function for threading protein sequence through the folding motif
-
Bryant SH, Lawrence CE. An empirical energy function for threading protein sequence through the folding motif. Proteins 1993;16:92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
24
-
-
0027302043
-
Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures
-
Ouzounis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J Mol Biol 1993;232:805-825.
-
(1993)
J Mol Biol
, vol.232
, pp. 805-825
-
-
Ouzounis, C.1
Sander, C.2
Scharf, M.3
Schneider, R.4
-
25
-
-
0026704815
-
Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
-
Sippl MJ, Weitckus S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins 1992;13:258-271.
-
(1992)
Proteins
, vol.13
, pp. 258-271
-
-
Sippl, M.J.1
Weitckus, S.2
-
26
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones TD. Taylor WR. Thronton JM. A new approach to protein fold recognition. Nature 1992;358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, T.D.1
Taylor, W.R.2
Thronton, J.M.3
-
27
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A, Kolinski A, Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 1992;227:227-238.
-
(1992)
J Mol Biol
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Kolinski, A.2
Skolnick, J.3
-
28
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher AJP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994;235:1598-1613.
-
(1994)
J Mol Biol
, vol.235
, pp. 1598-1613
-
-
Kocher, A.J.P.1
Rooman, M.J.2
Wodak, S.J.3
-
29
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luethy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-169.
-
(1991)
Science
, vol.253
, pp. 164-169
-
-
Bowie, J.U.1
Luethy, R.2
Eisenberg, D.3
-
30
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich M, Lackner P, Weitckus S, Floeckner H, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 1990;216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Gottsbacher, K.5
Casari, G.6
Sippl, M.J.7
-
31
-
-
0025851973
-
Prediction of protein folding from amino acid sequence over discrete conformation spaces
-
Crippen GM. Prediction of protein folding from amino acid sequence over discrete conformation spaces. Biochemistry 1991;30:4232-4237.
-
(1991)
Biochemistry
, vol.30
, pp. 4232-4237
-
-
Crippen, G.M.1
-
32
-
-
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;55:1005-1013.
-
(2004)
Proteins
, vol.55
, pp. 1005-1013
-
-
Zhou, H.1
Zhou, Y.2
-
33
-
-
0035866002
-
Defrosting the frozen approximation: PROSPECTOR - a new approach to threading
-
Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331.
-
(2001)
Proteins
, vol.42
, pp. 319-331
-
-
Skolnick, J.1
Kihara, D.2
-
34
-
-
0030310317
-
-
Fischer D, Elofsson A, Rice DW, LeGrand S, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In: Hunter L, Klein T, editors. Biocomputing: Proceedings of the 1996 Pacific Symposium. Singapore: World Scientific Publishing Co. Pac Symp Biocomput 1996;300-318.
-
Fischer D, Elofsson A, Rice DW, LeGrand S, Eisenberg D. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In: Hunter L, Klein T, editors. Biocomputing: Proceedings of the 1996 Pacific Symposium. Singapore: World Scientific Publishing Co. Pac Symp Biocomput 1996;300-318.
-
-
-
-
35
-
-
0028579433
-
Protein structural similarities predicted by a sequence-structure compatibility method
-
Matsuo Y, Nishikawa K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 1994;3:2055-2063.
-
(1994)
Protein Sci
, vol.3
, pp. 2055-2063
-
-
Matsuo, Y.1
Nishikawa, K.2
-
36
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures in CASP6
-
Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005;61 (Suppl 7):91-98.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
37
-
-
0032525159
-
Are knowledgebased potentials derived from protein structure sets discriminative with respect to amino acid types?
-
Sunyaev SR, Eisenhaber F, Argos P, Kuznetsov EN, Tumanyan VG. Are knowledgebased potentials derived from protein structure sets discriminative with respect to amino acid types? Proteins 1998;31:225-246.
-
(1998)
Proteins
, vol.31
, pp. 225-246
-
-
Sunyaev, S.R.1
Eisenhaber, F.2
Argos, P.3
Kuznetsov, E.N.4
Tumanyan, V.G.5
-
38
-
-
44349158108
-
-
Eisenhaber F, Sunyaev SR, Tumanyan VG, Kuznetsov EN. Measuring generality of knowledge-based potentials extracted from protein structure sets. In: (Galperin MY, Koonin EV, editors). Frontiers in computational genomics, 3. Wymondham, Norfolk, UK: Horizon Scientific Press; 2003. pp 57-87. Functional genomics series (Saier MH, Jr).
-
Eisenhaber F, Sunyaev SR, Tumanyan VG, Kuznetsov EN. Measuring generality of knowledge-based potentials extracted from protein structure sets. In: (Galperin MY, Koonin EV, editors). Frontiers in computational genomics, Vol. 3. Wymondham, Norfolk, UK: Horizon Scientific Press; 2003. pp 57-87. Functional genomics series (Saier MH, Jr).
-
-
-
-
39
-
-
44349127013
-
Side chain orientations as a characteristic of native protein structure
-
Managadze G, Vishnepolsky B, Pirtskhalava M. Side chain orientations as a characteristic of native protein structure. J Biol Phys Chem 2004;4:33-38.
-
(2004)
J Biol Phys Chem
, vol.4
, pp. 33-38
-
-
Managadze, G.1
Vishnepolsky, B.2
Pirtskhalava, M.3
-
40
-
-
44349128163
-
Threading potential based on the orientation of side chains in relation to hydrophobic cores centres and on the distance of residues from geometrical center of protein globule
-
Managadze G, Vishnepolsky B, Lomidze L, Grigolava M, Pirtskhalava M. Threading potential based on the orientation of side chains in relation to hydrophobic cores centres and on the distance of residues from geometrical center of protein globule. Proc Georgian Acad Sci Biol Ser 2004;2:20-28.
-
(2004)
Proc Georgian Acad Sci Biol Ser
, vol.2
, pp. 20-28
-
-
Managadze, G.1
Vishnepolsky, B.2
Lomidze, L.3
Grigolava, M.4
Pirtskhalava, M.5
-
42
-
-
0032948129
-
Enhanced protein fold recognition using secondary structure information from NMR
-
Ayers DJ. Gooley PR., Widmer-Cooper A, Torda AE. Enhanced protein fold recognition using secondary structure information from NMR. Protein Sci 1999;8:1127-1133.
-
(1999)
Protein Sci
, vol.8
, pp. 1127-1133
-
-
Ayers, D.J.1
Gooley, P.R.2
Widmer-Cooper, A.3
Torda, A.E.4
-
43
-
-
0029996162
-
Incorporation of long-distance interactions into a secondary structure prediction algorithm
-
Frishman D, Argos P. Incorporation of long-distance interactions into a secondary structure prediction algorithm. Protein Eng 1996; 9:133-142.
-
(1996)
Protein Eng
, vol.9
, pp. 133-142
-
-
Frishman, D.1
Argos, P.2
-
44
-
-
0034615787
-
Structure-based evaluation of sequence comparison and fold recognition alignment accuracy
-
Domingues FS, Lackner P, Andreeva A, Sippl MJ. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J Mol Biol 2000;297:1003-1013.
-
(2000)
J Mol Biol
, vol.297
, pp. 1003-1013
-
-
Domingues, F.S.1
Lackner, P.2
Andreeva, A.3
Sippl, M.J.4
-
45
-
-
0029785147
-
Mapping the protein universe
-
Holm L, Sander C. Mapping the protein universe. Science 1996;273:595-602.
-
(1996)
Science
, vol.273
, pp. 595-602
-
-
Holm, L.1
Sander, C.2
-
46
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needelman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 1970;48:443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needelman, S.B.1
Wunsch, C.D.2
-
47
-
-
0019887799
-
The identification of common molecular subsequences
-
Smith TF, Waterman MS. The identification of common molecular subsequences. J Mol Biol 1981;147:195-197.
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
48
-
-
0025878149
-
Amino acid substitution matrices from an information theoretic perspective
-
Altshul SF. Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 1991;219:555-565.
-
(1991)
J Mol Biol
, vol.219
, pp. 555-565
-
-
Altshul, S.F.1
-
49
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 2005;15:285-289.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 285-289
-
-
Moult, J.1
-
50
-
-
0028063257
-
Polar and non-polar atomic environments in the protein core: Implication for folding and binding
-
Koehl P, Delarue M. Polar and non-polar atomic environments in the protein core: implication for folding and binding. Proteins 1994;20:264-278.
-
(1994)
Proteins
, vol.20
, pp. 264-278
-
-
Koehl, P.1
Delarue, M.2
-
51
-
-
34248328316
-
A protein folding potential that places the native states of a large number of proteins near a local minimum
-
Chhajer M, Crippen GM. A protein folding potential that places the native states of a large number of proteins near a local minimum. BMC Struct Biol 2002;2:4
-
(2002)
BMC Struct Biol
, vol.2
, pp. 4
-
-
Chhajer, M.1
Crippen, G.M.2
-
52
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996;256:623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
53
-
-
3342936478
-
A comprehensive analysis of 40 blind protein structure predictions
-
Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol 2002;2:3.
-
(2002)
BMC Struct Biol
, vol.2
, pp. 3
-
-
Samudrala, R.1
Levitt, M.2
-
54
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
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.
-
(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
-
55
-
-
0032871834
-
Finding families for genomic ORFans. The role of bioinformatics and structural biology
-
Fischer D, Eisenberg D. Finding families for genomic ORFans. The role of bioinformatics and structural biology. Bioinformatics 1999;15:759-762.
-
(1999)
Bioinformatics
, vol.15
, pp. 759-762
-
-
Fischer, D.1
Eisenberg, D.2
-
56
-
-
0037228878
-
Twenty thousand ORFan microbial protein families for the biologist?
-
Siew N, Fischer D. Twenty thousand ORFan microbial protein families for the biologist? Structure 2003;11:7-9.
-
(2003)
Structure
, vol.11
, pp. 7-9
-
-
Siew, N.1
Fischer, D.2
-
57
-
-
33746639718
-
Emergence of protein fold families through rational design
-
Ding F, Dokholyan NV. Emergence of protein fold families through rational design. PLoS Comput Biol 2006;2:e85.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Ding, F.1
Dokholyan, N.V.2
|