-
1
-
-
85038184314
-
Effect of secondary structure prediction on protein fold recognition and database search
-
Akutsu T, Asai K, Hagiya M, Kuhara S, Miyano S, Nakai K, eds. Tokyo, Japan: Universal Academy Press
-
Alexandrov NN, Solovyev VV. 1996. Effect of secondary structure prediction on protein fold recognition and database search. In. Akutsu T, Asai K, Hagiya M, Kuhara S, Miyano S, Nakai K, eds. Genome informatics 1996. Tokyo, Japan: Universal Academy Press.
-
(1996)
Genome Informatics 1996
-
-
Alexandrov, N.N.1
Solovyev, V.V.2
-
2
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GTB, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.T.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
3
-
-
0025341237
-
Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures
-
Bowie JU, Clarke ND, Pabo CO, Sauer T. 1990. Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures. Proteins 7:257-264.
-
(1990)
Proteins
, vol.7
, pp. 257-264
-
-
Bowie, J.U.1
Clarke, N.D.2
Pabo, C.O.3
Sauer, T.4
-
4
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Lüthy R, Eisenberg D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
5
-
-
0027318317
-
An empirical energy function for threading protein sequence through folding motif
-
Bryant SH, Lawrence CE. 1993. An empirical energy function for threading protein sequence through folding motif. Proteins 16:92-112.
-
(1993)
Proteins
, vol.16
, pp. 92-112
-
-
Bryant, S.H.1
Lawrence, C.E.2
-
6
-
-
16044367245
-
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
-
Bult CJ et al. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 275:1058-1073.
-
(1996)
Science
, vol.275
, pp. 1058-1073
-
-
Bult, C.J.1
-
7
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C, Lesk AM. 1987. The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826.
-
(1987)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
8
-
-
0029959722
-
Failures of inverse folding and threading with gapped alignment
-
Crippen GM. 1996. Failures of inverse folding and threading with gapped alignment. Proteins 26:167-171.
-
(1996)
Proteins
, vol.26
, pp. 167-171
-
-
Crippen, G.M.1
-
9
-
-
0030595366
-
Multiple sequence information for threading algorithms
-
Defay TR, Cohen FE. 1996. Multiple sequence information for threading algorithms. J Mol Biol 262:314-323.
-
(1996)
J Mol Biol
, vol.262
, pp. 314-323
-
-
Defay, T.R.1
Cohen, F.E.2
-
10
-
-
0030724017
-
Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium
-
Fischer D, Eisenberg D. 1997. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 94:11929-11934.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 11929-11934
-
-
Fischer, D.1
Eisenberg, D.2
-
11
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gilis D, Rooman M. 1996. Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J Mol Biol 1996:1112-1126.
-
(1996)
J Mol Biol
, vol.1996
, pp. 1112-1126
-
-
Gilis, D.1
Rooman, M.2
-
12
-
-
0029117449
-
In search of the ideal protein sequence
-
Godzik A. 1995. In search of the ideal protein sequence. Protein Eng 8:409-416.
-
(1995)
Protein Eng
, vol.8
, pp. 409-416
-
-
Godzik, A.1
-
13
-
-
0026726481
-
Topology fingerprint approach to the inverse protein folding problem
-
Godzik A, Skolnick J, Kolinski A. 1992. Topology fingerprint approach to the inverse protein folding problem. J Mol Biol 227:227-238.
-
(1992)
J Mol Biol
, vol.227
, pp. 227-238
-
-
Godzik, A.1
Skolnick, J.2
Kolinski, A.3
-
14
-
-
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, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. 1990. 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 216:167-180.
-
(1990)
J Mol Biol
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
15
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm L, Sander C. 1993. Protein structure comparison by alignment of distance matrices. J Mol Biol 233:123-138.
-
(1993)
J Mol Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
17
-
-
0028318094
-
Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
-
Kocher JA, Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
-
(1994)
J Mol Biol
, vol.235
, pp. 1598-1613
-
-
Kocher, J.A.1
Rooman, M.J.2
Wodak, S.J.3
-
18
-
-
0028818340
-
Protein structure prediction by threading methods: Evaluation of current technologies
-
Lamer M-R, Rooman MJ, Wodak SJ. 1995. Protein structure prediction by threading methods: Evaluation of current technologies. Proteins 23:337-355.
-
(1995)
Proteins
, vol.23
, pp. 337-355
-
-
Lamer, M.-R.1
Rooman, M.J.2
Wodak, S.J.3
-
19
-
-
0031307020
-
Competitive assessment of protein fold recognition and alignment accuracy
-
Levitt M. 1997. Competitive assessment of protein fold recognition and alignment accuracy. Proteins suppl 1:92-104.
-
(1997)
Proteins Suppl
, vol.1
, pp. 92-104
-
-
Levitt, M.1
-
20
-
-
0028033123
-
Learning about protein folding via potential functions
-
Maiorov VN, Crippen GM. 1994. Learning about protein folding via potential functions. Proteins 20:167-173.
-
(1994)
Proteins
, vol.20
, pp. 167-173
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
22
-
-
0029083544
-
Detection of 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions
-
Matsuo Y, Nakamura H, Nishikawa K. 1995. Detection of 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions. J Biochem (Tokyo) 118:137-148.
-
(1995)
J Biochem (Tokyo)
, vol.118
, pp. 137-148
-
-
Matsuo, Y.1
Nakamura, H.2
Nishikawa, K.3
-
23
-
-
0028579433
-
Protein structural similarities predicted by a sequence-structure compatibility method
-
Matsuo Y, Nishikawa K. 1994. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 3:2055-2063.
-
(1994)
Protein Sci
, vol.3
, pp. 2055-2063
-
-
Matsuo, Y.1
Nishikawa, K.2
-
24
-
-
0028075953
-
Protein stability for single substitution mutants and the extent of local compactness in the denatured state
-
Miyazawa S, Jernigan RL. 1994. Protein stability for single substitution mutants and the extent of local compactness in the denatured state. Protein Eng 7:1209-1220.
-
(1994)
Protein Eng
, vol.7
, pp. 1209-1220
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
25
-
-
0028961335
-
Scop: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. 1995. Scop: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
-
(1995)
J Mol Biol
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
26
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman SB, Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48-443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
27
-
-
0027504808
-
Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies
-
Nishikawa K, Matsuo Y. 1993. Development of pseudoenergy potentials for assessing protein 3-D-1-D compatibility and detecting weak homologies. Protein Eng 6:811-820.
-
(1993)
Protein Eng
, vol.6
, pp. 811-820
-
-
Nishikawa, K.1
Matsuo, Y.2
-
28
-
-
0029003770
-
Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H
-
Ota M, Kanaya S, Nishikawa K. 1995. Desk-top analysis of the structural stability of various point mutations introduced into ribonuclease H. J Mol Biol 248:733-738.
-
(1995)
J Mol Biol
, vol.248
, pp. 733-738
-
-
Ota, M.1
Kanaya, S.2
Nishikawa, K.3
-
29
-
-
0030904226
-
Assessment of the pseudo-energy potential by the best-five test: A new use of the three-dimensional profiles of proteins
-
Ota M, Nishikawa K. 1997. Assessment of the pseudo-energy potential by the best-five test: A new use of the three-dimensional profiles of proteins. Protein Eng 10:339-351.
-
(1997)
Protein Eng
, vol.10
, pp. 339-351
-
-
Ota, M.1
Nishikawa, K.2
-
30
-
-
0027302043
-
Prediction of protein structure by evaluation of sequence-structure fitness: Aligning sequences to contact profiles derived from 3D structures
-
Ouzounis C, Sander C, Scharf M, Schneider RJ. 1993. Prediction of protein structure by evaluation of sequence-structure fitness: aligning sequences to contact profiles derived from 3D structures. J Mol Biol 232:805-825.
-
(1993)
J Mol Biol
, vol.232
, pp. 805-825
-
-
Ouzounis, C.1
Sander, C.2
Scharf, M.3
Schneider, R.J.4
-
31
-
-
0029563695
-
Are database-derived potentials valid for scoring both forward and inverted protein folding?
-
Rooman MJ, Wodak SJ. 1995. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 8:849-858.
-
(1995)
Protein Eng
, vol.8
, pp. 849-858
-
-
Rooman, M.J.1
Wodak, S.J.2
-
32
-
-
0031844330
-
Fold and function predictions for Mycoplasma genitalium proteins
-
Rychlewski L, Zhang B, Godzik A. 1998. Fold and function predictions for Mycoplasma genitalium proteins. Folding Design 3:229-238.
-
(1998)
Folding Design
, vol.3
, pp. 229-238
-
-
Rychlewski, L.1
Zhang, B.2
Godzik, A.3
-
33
-
-
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. 1990. 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 213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
34
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
35
-
-
0024349252
-
Protein structure alignment
-
Taylor WR, Orengo CA. 1989. Protein structure alignment. J Mol Biol 208: 1-22.
-
(1989)
J Mol Biol
, vol.208
, pp. 1-22
-
-
Taylor, W.R.1
Orengo, C.A.2
-
36
-
-
0029554779
-
Protein fold recognition by threading: Comparison of algorithms and analysis of results
-
Wasthead DR, Collura VP, Eldridge MD, Firth MA, Li J, Murray CW. 1995. Protein fold recognition by threading: Comparison of algorithms and analysis of results. Protein Eng 8:1197-1204.
-
(1995)
Protein Eng
, vol.8
, pp. 1197-1204
-
-
Wasthead, D.R.1
Collura, V.P.2
Eldridge, M.D.3
Firth, M.A.4
Li, J.5
Murray, C.W.6
-
37
-
-
0027458885
-
Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold
-
Wilmanns M, Eisenberg D. 1993. Three-dimensional profiles from residue-pair preferences: Identification of sequences with β/α-barrel fold. Proc Natl Acad Sci USA 90:1379-1383.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 1379-1383
-
-
Wilmanns, M.1
Eisenberg, D.2
|