-
1
-
-
0000977124
-
Relative orientation of close-packed beta-pleated sheets in proteins
-
Chothia C, Janin J. Relative orientation of close-packed beta-pleated sheets in proteins. Proc Natl Acad Sci USA 1981;78:4146-4150.
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, pp. 4146-4150
-
-
Chothia, C.1
Janin, J.2
-
2
-
-
0020485895
-
Orthogonal packing of beta-pleated sheets in proteins
-
Chothia C, Janin J. Orthogonal packing of beta-pleated sheets in proteins. Biochemistry 1982;21:3955-3965.
-
(1982)
Biochemistry
, vol.21
, pp. 3955-3965
-
-
Chothia, C.1
Janin, J.2
-
3
-
-
0027918655
-
Unusual structural features in the parallel beta-helix in pectate lyases
-
Yoder MD, Lietzke S, Jurnack F. Unusual structural features in the parallel beta-helix in pectate lyases. Structure 1993;1:241-251.
-
(1993)
Structure
, vol.1
, pp. 241-251
-
-
Yoder, M.D.1
Lietzke, S.2
Jurnack, F.3
-
4
-
-
0035543109
-
The architecture of parallel beta-helices and related folds
-
Jenkins J, Pickersgill R. The architecture of parallel beta-helices and related folds. Prog Biophys Mol Biol 2001;77:111-175.
-
(2001)
Prog Biophys Mol Biol
, vol.77
, pp. 111-175
-
-
Jenkins, J.1
Pickersgill, R.2
-
5
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;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
-
6
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. Twilight zone of protein sequence alignments. Protein Eng 1999;12:85-94.
-
(1999)
Protein Eng
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
7
-
-
0033550256
-
Effective use of sequence correlation and conservation in fold recognition
-
Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999;293:1221-1239.
-
(1999)
J Mol Biol
, vol.293
, pp. 1221-1239
-
-
Olmea, O.1
Rost, B.2
Valencia, A.3
-
8
-
-
0036681397
-
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory
-
Steward RE, Thornton JM. Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins 2002;48;178-191.
-
(2002)
Proteins
, vol.48
, pp. 178-191
-
-
Steward, R.E.1
Thornton, J.M.2
-
9
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
-
(1993)
J Mol Biol
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
10
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:95-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 95-202
-
-
Jones, D.T.1
-
11
-
-
0035703008
-
Assessment of novel fold targets in casp4: Predictions of three-dimensional structures, secondary structures and interresidue contacts
-
Lesk AM, LoConte L, Hubbard TJP. Assessment of novel fold targets in casp4: predictions of three-dimensional structures, secondary structures and interresidue contacts. Proteins Suppl 2001;5:98-118.
-
(2001)
Proteins Suppl
, vol.5
, pp. 98-118
-
-
Lesk, A.M.1
LoConte, L.2
Hubbard, T.J.P.3
-
12
-
-
10744226366
-
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
-
Bradley P, Chivian D, Meiler J, Misura KM, Rohl C, Schief W, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss C, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins 2003;53:457-468.
-
(2003)
Proteins
, vol.53
, pp. 457-468
-
-
Bradley, P.1
Chivian, D.2
Meiler, J.3
Misura, K.M.4
Rohl, C.5
Schief, W.6
Wedemeyer, W.J.7
Schueler-Furman, O.8
Murphy, P.9
Schonbrun, J.10
Strauss, C.11
Baker, D.12
-
13
-
-
0036606453
-
Ab initio prediction of protein structure using LINUS
-
Srinivasan R, Rose GD. Ab initio prediction of protein structure using LINUS. Proteins 2002;47:489-495.
-
(2002)
Proteins
, vol.47
, pp. 489-495
-
-
Srinivasan, R.1
Rose, G.D.2
-
14
-
-
0029145638
-
Predicting coiled coils by use of pairwise residue correlations
-
Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci USA 1995;92:8259-8263.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 8259-8263
-
-
Berger, B.1
Wilson, D.B.2
Wolf, E.3
Tonchev, T.4
Milla, M.5
Kim, P.S.6
-
15
-
-
4143058720
-
Predicting specificity in bZIP coiled-coil protein interactions
-
Fong J, Keating AE, Singh MS. Predicting specificity in bZIP coiled-coil protein interactions. Genome Biol 2004;5:R11.
-
(2004)
Genome Biol
, vol.5
-
-
Fong, J.1
Keating, A.E.2
Singh, M.S.3
-
16
-
-
0035910068
-
BETAWRAP: Successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens
-
Bradley P, Cowen L, Menke M, King J, Berger B. BETAWRAP: successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci USA 2001;98:14819-14824.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 14819-14824
-
-
Bradley, P.1
Cowen, L.2
Menke, M.3
King, J.4
Berger, B.5
-
17
-
-
0036107627
-
Predicting the beta-helix fold from protein sequence data
-
Cowen L, Bradley P, Menke M, King J, Berger B. Predicting the beta-helix fold from protein sequence data. J Comput Biol 2002;9:261-276.
-
(2002)
J Comput Biol
, vol.9
, pp. 261-276
-
-
Cowen, L.1
Bradley, P.2
Menke, M.3
King, J.4
Berger, B.5
-
18
-
-
2442581305
-
-
RECOMB; San Diego, CA
-
Menke M, Scanlon, E., King, J., Berger, B., Cowen, L. Wrap-and-pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. RECOMB; San Diego, CA; 2004. p 298-307.
-
(2004)
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils
, pp. 298-307
-
-
Menke, M.1
Scanlon, E.2
King, J.3
Berger, B.4
Cowen, L.5
-
19
-
-
26444535298
-
-
RECOMB; Cambridge, MA
-
Liu Y, Carbonell J, Weigele P, Gopalakrishna V. Segmentation conditional random fields (SCRFs): a new approach to protein fold recognition. RECOMB; Cambridge, MA; 2005. p 408-422.
-
(2005)
Segmentation Conditional Random Fields (SCRFs): A New Approach to Protein Fold Recognition
, pp. 408-422
-
-
Liu, Y.1
Carbonell, J.2
Weigele, P.3
Gopalakrishna, V.4
-
21
-
-
0036307493
-
Within the twilight zone: A sensitive profile-profile comparison tool based on information theory
-
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.
-
(2002)
J Mol Biol
, vol.315
, pp. 1257-1275
-
-
Yona, G.1
Levitt, M.2
-
22
-
-
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;287:797-815.
-
(1999)
J Mol Biol
, vol.287
, pp. 797-815
-
-
Jones, D.T.1
-
24
-
-
0032613429
-
Threading with explicit models for evolutionary conservation of structure and sequence
-
Panchenko A, Marchler-Bauer A, Bryant SH. Threading with explicit models for evolutionary conservation of structure and sequence. Proteins Suppl 1999;3:133-140.
-
(1999)
Proteins Suppl
, vol.3
, pp. 133-140
-
-
Panchenko, A.1
Marchler-Bauer, A.2
Bryant, S.H.3
-
25
-
-
23844520274
-
Wrap-and-Pack: A new paradigm for beta structural motif recognition with application to recognizing beta trefoils
-
Menke M, King J, Berger B, Cowen L. Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils. J Comput Biol 2005;12:777-795.
-
(2005)
J Comput Biol
, vol.12
, pp. 777-795
-
-
Menke, M.1
King, J.2
Berger, B.3
Cowen, L.4
-
26
-
-
0027160197
-
A backbone dependent rotamer library for proteins: Application to side-chain prediction
-
Dunbrack RLJ, Karplus M. A backbone dependent rotamer library for proteins: application to side-chain prediction. J Mol Biol 1993;230:543-571.
-
(1993)
J Mol Biol
, vol.230
, pp. 543-571
-
-
Dunbrack, R.L.J.1
Karplus, M.2
-
27
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu AA, Shelenkov AA, Dunbrack RLJ. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.J.3
-
28
-
-
0034663738
-
Protein threading using PROSPECT: Design and evaluation
-
Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000;40:343-354.
-
(2000)
Proteins
, vol.40
, pp. 343-354
-
-
Xu, Y.1
Xu, D.2
-
29
-
-
0032605828
-
Processing and analysis of CASP3 protein structure predictions
-
Zemla A, Venclovas C, Moult J, Fidelis K. Processing and analysis of CASP3 protein structure predictions. Proteins 1999;37(S3):22-29.
-
(1999)
Proteins
, vol.37
, Issue.S3
, pp. 22-29
-
-
Zemla, A.1
Venclovas, C.2
Moult, J.3
Fidelis, K.4
-
30
-
-
0031576989
-
Prediction of protein sice-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
Bower MJ, Cohen FE, Dunbrack RLJ. Prediction of protein sice-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
-
(1997)
J Mol Biol
, vol.267
, pp. 1268-1282
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack, R.L.J.3
-
31
-
-
0032613301
-
Comparative modeling of casp3 targets using PSI-BLAST and SCWRL
-
Dunbrack RLJ. Comparative modeling of casp3 targets using PSI-BLAST and SCWRL. Proteins Suppl 1999;3:81-87.
-
(1999)
Proteins Suppl
, vol.3
, pp. 81-87
-
-
Dunbrack, R.L.J.1
-
32
-
-
0031720234
-
Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
-
Huang ES, Koehl P, Levitt M, Pappu RV, Ponder JW. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins 1998;33:204-217.
-
(1998)
Proteins
, vol.33
, pp. 204-217
-
-
Huang, E.S.1
Koehl, P.2
Levitt, M.3
Pappu, R.V.4
Ponder, J.W.5
-
33
-
-
0242369082
-
RAPTOR: Optimal protein threading by linear programming
-
Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 2003;1:95-117.
-
(2003)
J Bioinform Comput Biol
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
34
-
-
13544259023
-
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core
-
Czerwinski EW, Midoro-Horiuti T, White MA, Brooks EG, Goldblum RM. Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core. J Biol Chem 2005;280:3740-3746.
-
(2005)
J Biol Chem
, vol.280
, pp. 3740-3746
-
-
Czerwinski, E.W.1
Midoro-Horiuti, T.2
White, M.A.3
Brooks, E.G.4
Goldblum, R.M.5
-
35
-
-
1942437434
-
The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway
-
Clantin B, Hodak H, Willery E, Locht C, Jacob-Dubuisson F, Villeret V. The crystal structure of filamentous hemagglutinin secretion domain and its implications for the two-partner secretion pathway. Proc Natl Acad Sci USA 2004;101:6194-6199.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6194-6199
-
-
Clantin, B.1
Hodak, H.2
Willery, E.3
Locht, C.4
Jacob-Dubuisson, F.5
Villeret, V.6
-
36
-
-
0027463701
-
Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms
-
Shchelkunov SN, BLinov VM, Sandakhchiev LS. Genes of variola and vaccinia viruses necessary to overcome the host protective mechanisms. FEBS Lett 1993;319:80-83.
-
(1993)
FEBS Lett
, vol.319
, pp. 80-83
-
-
Shchelkunov, S.N.1
Blinov, V.M.2
Sandakhchiev, L.S.3
-
37
-
-
1242340413
-
Beta-helix is a likely core structure of yeast prion sup35 and amyloid fibers
-
Kishimoto A, Hasegawa K, Suzuki H, Taguchi H, Namba K, Yoshida M. Beta-helix is a likely core structure of yeast prion sup35 and amyloid fibers. Biochem Biophys Res Commun 2004;315:739-745.
-
(2004)
Biochem Biophys Res Commun
, vol.315
, pp. 739-745
-
-
Kishimoto, A.1
Hasegawa, K.2
Suzuki, H.3
Taguchi, H.4
Namba, K.5
Yoshida, M.6
-
38
-
-
0028095571
-
Crystal structure of p22 tailspike protein: Interdigitated subunits in a thermostable trimer
-
Steinbacher S, Seckler R, Miller S, Steipe B, Huber R, Reinemer P. Crystal structure of p22 tailspike protein: interdigitated subunits in a thermostable trimer. Science 1994;265:383-386.
-
(1994)
Science
, vol.265
, pp. 383-386
-
-
Steinbacher, S.1
Seckler, R.2
Miller, S.3
Steipe, B.4
Huber, R.5
Reinemer, P.6
-
39
-
-
0031570284
-
Two crystal structures of pectin lyase a from aspergillus reveal a ph driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases
-
Mayans O, Scott M, Connerton I, Gravesen T, Benen J, Visser J, Pickersgill R, Jenkns J. Two crystal structures of pectin lyase A from aspergillus reveal a ph driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure 1997;5:677-689.
-
(1997)
Structure
, vol.5
, pp. 677-689
-
-
Mayans, O.1
Scott, M.2
Connerton, I.3
Gravesen, T.4
Benen, J.5
Visser, J.6
Pickersgill, R.7
Jenkns, J.8
-
40
-
-
0029988488
-
Structure of bordetella pertussis virulence factor p.69 pertactin
-
Emsley P, Charles IG, Fairweather NF, Isaacs NW. Structure of bordetella pertussis virulence factor p.69 pertactin. Nature 1996;381:90-92.
-
(1996)
Nature
, vol.381
, pp. 90-92
-
-
Emsley, P.1
Charles, I.G.2
Fairweather, N.F.3
Isaacs, N.W.4
-
41
-
-
0029764093
-
Crystal structure of phage p22 tailspike protein complexed with Salmonella Sp. o-antigen receptors
-
Steinbacher S, Baxa U, Miller S, Weintraub A, Seckler R, Huber R. Crystal structure of phage p22 tailspike protein complexed with Salmonella Sp. o-antigen receptors Proc Natl Acad Sci USA 1996;93:10584-10588.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 10584-10588
-
-
Steinbacher, S.1
Baxa, U.2
Miller, S.3
Weintraub, A.4
Seckler, R.5
Huber, R.6
-
42
-
-
0028280034
-
Meal patterns in response to the intracerebroventricular administration of interleukin-1 beta in rats
-
Plata-Salaman CR. Meal patterns in response to the intracerebroventricular administration of interleukin-1 beta in rats. Physiol Behav 1994;55:727-733.
-
(1994)
Physiol Behav
, vol.55
, pp. 727-733
-
-
Plata-Salaman, C.R.1
-
43
-
-
0023216442
-
Interleukin 1 is potent modulator of insulin secretion from isolated rat islets of Langerhans
-
Comens PG, Wolf BA, Unanue ER, Lacy PE, McDaniel ML. Interleukin 1 is potent modulator of insulin secretion from isolated rat islets of Langerhans. Diabetes 1987;36:963-970.
-
(1987)
Diabetes
, vol.36
, pp. 963-970
-
-
Comens, P.G.1
Wolf, B.A.2
Unanue, E.R.3
Lacy, P.E.4
McDaniel, M.L.5
-
44
-
-
0031056969
-
A purified protein from Salmonella typhimurium inhibits high-affinity interleukin-2 receptor expression on CTLL-2 cells
-
Arai T, Matsui K. A purified protein from Salmonella typhimurium inhibits high-affinity interleukin-2 receptor expression on CTLL-2 cells. FEMS Immunol Med Microbiol 1997;17:155-160.
-
(1997)
FEMS Immunol Med Microbiol
, vol.17
, pp. 155-160
-
-
Arai, T.1
Matsui, K.2
-
45
-
-
9144257886
-
The Pfam protein families database
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acids Res 2004;32:D138-D141.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Griffiths-Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.10
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
46
-
-
0035072551
-
Clustering of highly homologous sequences to reduce the size of large protein databases
-
Li W, Jaroszewski L, Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001;17:282-283.
-
(2001)
Bioinformatics
, vol.17
, pp. 282-283
-
-
Li, W.1
Jaroszewski, L.2
Godzik, A.3
-
47
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
48
-
-
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
-
49
-
-
0032964297
-
Blast 2 sequences-a new tool for comparing protein and nucleotide sequences
-
Tatusova TA, Madden TL. Blast 2 sequences-a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999;174:247-250.
-
(1999)
FEMS Microbiol Lett
, vol.174
, pp. 247-250
-
-
Tatusova, T.A.1
Madden, T.L.2
|