-
1
-
-
32144449896
-
Mean curvature as a major determinant of beta-sheet propensity
-
E. Koh, T. Kim, and H.S. Cho, "Mean Curvature as a Major Determinant of Beta-Sheet Propensity," Bioinformatics, vol. 22, pp. 297-302, 2006.
-
(2006)
Bioinformatics
, vol.22
, pp. 297-302
-
-
Koh, E.1
Kim, T.2
Cho, H.S.3
-
2
-
-
0034674168
-
The anatomy of protein beta-sheet topology
-
C. Zhang and S. Kim, "The Anatomy of Protein Beta-Sheet Topology," J. Molecular Biology, vol. 299, pp. 1075-1089, 2000.
-
(2000)
J. Molecular Biology
, vol.299
, pp. 1075-1089
-
-
Zhang, C.1
Kim, S.2
-
3
-
-
0032815297
-
Context-dependence of amino acid residue pairing in antiparallel/3-sheets
-
S.M. Zaremba and L.M. Gregoret, "Context-Dependence of Amino Acid Residue Pairing in Antiparallel/3-Sheets," J. Molecular Biology, vol. 291, pp. 463-479, 1999.
-
(1999)
J. Molecular Biology
, vol.291
, pp. 463-479
-
-
Zaremba, S.M.1
Gregoret, L.M.2
-
4
-
-
0036643499
-
Distributions of beta sheets in proteins with application to structure prediction
-
I. Ruczinski, C. Kooperberg, R. Bonneau, and D. Baker, "Distributions of Beta Sheets in Proteins with Application to Structure Prediction," Proteins: Structure, Function and Genetics, vol. 48, pp. 85-97, 2002.
-
(2002)
Proteins: Structure, Function and Genetics
, vol.48
, pp. 85-97
-
-
Ruczinski, I.1
Kooperberg, C.2
Bonneau, R.3
Baker, D.4
-
5
-
-
0034703088
-
Modulating protein folding rates in vivo and in vitro by side chain interactions between the parallel beta strands of green fluorescent protein
-
J.S. Merkel and L. Regan, "Modulating Protein Folding Rates In Vivo and In Vitro by Side Chain Interactions between the Parallel Beta Strands of Green Fluorescent Protein," J. Biological Chemistry, vol. 275, pp. 29200-29206, 2000.
-
(2000)
J. Biological Chemistry
, vol.275
, pp. 29200-29206
-
-
Merkel, J.S.1
Regan, L.2
-
6
-
-
0035793216
-
Contributions of residue pairing to beta-sheet formation: Conservation and covariation of amino acid residue pairs on antiparallel beta-strands
-
Y. Mandel-Gutfreund, S.M. Zaremba, and L.M. Gregoret, "Contributions of Residue Pairing to Beta-Sheet Formation: Conservation and Covariation of Amino Acid Residue Pairs on Antiparallel Beta-Strands," J. Molecular Biology, vol. 305, pp. 1145-1159, 2001.
-
(2001)
J. Molecular Biology
, vol.305
, pp. 1145-1159
-
-
Mandel-Gutfreund, Y.1
Zaremba, S.M.2
Gregoret, L.M.3
-
7
-
-
2642670311
-
Design of a 20-amino acid, three-stranded/3-sheet protein
-
T. Kortemme, M. Ramirez-Alvarado, and L. Serrano, "Design of a 20-Amino Acid, Three-Stranded/3-Sheet Protein," Science, vol. 281, pp. 253-256, 1998.
-
(1998)
Science
, vol.281
, pp. 253-256
-
-
Kortemme, T.1
Ramirez-Alvarado, M.2
Serrano, L.3
-
8
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
B. Kuhlman, G Dantas, G Ireton, G Varani, B. Stoddard, and D. Baker, "Design of a Novel Globular Protein Fold with Atomic-Level Accuracy," Science, vol. 302, pp. 1364-1368, 2003.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.3
Varani, G.4
Stoddard, B.5
Baker, D.6
-
9
-
-
0019317336
-
Specific recognition in the tertiary structure of beta-sheets of proteins
-
S. Lifson and C. Sander, "Specific Recognition in the Tertiary Structure of Beta-Sheets of Proteins," J. Molecular Biology, vol. 139, pp. 627-639, 1980.
-
(1980)
J. Molecular Biology
, vol.139
, pp. 627-639
-
-
Lifson, S.1
Sander, C.2
-
10
-
-
0027998757
-
Context is a major determinant of beta-sheet propensity
-
D.L. Minor and S. Kim, "Context Is a Major Determinant of Beta-Sheet Propensity," Nature, vol. 371, pp. 264-267, 1994.
-
(1994)
Nature
, vol.371
, pp. 264-267
-
-
Minor, D.L.1
Kim, S.2
-
11
-
-
0029058159
-
An analysis of side chain interactions and pair correlations within antiparallel beta-sheets: The differences between backbone hydrogen bonded and nonhydrogen bonded residue pairs
-
M.A. Wouters and P.M.G Curmi, "An Analysis of Side Chain Interactions and Pair Correlations within Antiparallel Beta-Sheets: The Differences between Backbone Hydrogen Bonded and Nonhydrogen Bonded Residue Pairs," Proteins: Structure, Function, and Genetics, vol. 22, pp. 119-131, 1995.
-
(1995)
Proteins: Structure, Function, and Genetics
, vol.22
, pp. 119-131
-
-
Wouters, M.A.1
Curmi, P.M.G.2
-
12
-
-
0033003903
-
Sequence specificity, statistical potentials, and three-dimensional structure prediction with selfcorrecting
-
H. Zhu and W. Braun, "Sequence Specificity, Statistical Potentials, and Three-Dimensional Structure Prediction with Selfcorrecting," Protein Science, vol. 8, pp. 326-342, 1999.
-
(1999)
Protein Science
, vol.8
, pp. 326-342
-
-
Zhu, H.1
Braun, W.2
-
13
-
-
0017610611
-
On the conformation of proteins: The handedness of the connection between parallel/3-strands
-
D.N. Woolfson, P.A. Evans, E.G. Hutchinson, and J.M. Thornton, "On the Conformation of Proteins: The Handedness of the Connection between Parallel/3-Strands," J. Molecular Biology, vol. 110, pp. 269-283, 1977.
-
(1977)
J. Molecular Biology
, vol.110
, pp. 269-283
-
-
Woolfson, D.N.1
Evans, P.A.2
Hutchinson, E.G.3
Thornton, J.M.4
-
14
-
-
0028792105
-
Guidelines for protein design: The energetics of (i sheet side chain interactions
-
C.K. Smith and L. Regan, "Guidelines for Protein Design: The Energetics of (i Sheet Side Chain Interactions," Science, vol. 270, pp. 980-982, 1995.
-
(1995)
Science
, vol.270
, pp. 980-982
-
-
Smith, C.K.1
Regan, L.2
-
15
-
-
0031735020
-
Determinants of strand register in antiparallel beta-sheets of proteins
-
E.G. Hutchinson, RB. Sessions, J.M. Thornton, and D.N. Woolfson, "Determinants of Strand Register in Antiparallel Beta-Sheets of Proteins," Protein Science, vol. 7, pp. 287-300, 1998.
-
(1998)
Protein Science
, vol.7
, pp. 287-300
-
-
Hutchinson, E.G.1
Sessions, R.B.2
Thornton, J.M.3
Woolfson, D.N.4
-
16
-
-
0028907511
-
Use of/3-strand interaction pseudo potentials in protein structure and modelling
-
T.J. Hubbard, "Use of/3-Strand Interaction Pseudo Potentials in Protein Structure and Modelling," Proc. 27th Hawaii Int'l Conf. System Sciences (HICSS '94), pp. 336-344, 1994.
-
(1994)
Proc. 27th Hawaii Int'l Conf. System Sciences (HICSS '94)
, pp. 336-344
-
-
Hubbard, T.J.1
-
17
-
-
0028874810
-
Fold recognition and ab initio structure predictions using hidden markov models and/3-strand pair potentials
-
T.J. Hubbard and J. Park, "Fold Recognition and Ab Initio Structure Predictions Using Hidden Markov Models and/3-Strand Pair Potentials," Proteins: Structure, Function, and Genetics, vol. 23, pp. 398-402, 1995.
-
(1995)
Proteins: Structure, Function, and Genetics
, vol.23
, pp. 398-402
-
-
Hubbard, T.J.1
Park, J.2
-
18
-
-
0030629054
-
Beta-sheet prediction using inter-strand residue pairs and refinement with hopfield neural network
-
M. Asogawa, "Beta-Sheet Prediction Using Inter-Strand Residue Pairs and Refinement with Hopfield Neural Network," Proc. Int'l Conf. Intelligent Systems for Molecular Biology, vol. 5, pp. 48-51, 1997.
-
(1997)
Proc. Int'l Conf. Intelligent Systems for Molecular Biology
, vol.5
, pp. 48-51
-
-
Asogawa, M.1
-
19
-
-
84864516302
-
Prediction of protein structure through evolution
-
J. Gasteiger and T. Engel, eds. Wiley
-
B. Rost, J. Liu, D. Przybylski, R Nair, K. Wrzeszczynski, H. Bigelow, and Y. Ofran, "Prediction of Protein Structure through Evolution," Handbook of Chemoinformatics from Data to Knowledge, J. Gasteiger and T. Engel, eds., pp. 1789-1811, Wiley, 2003.
-
(2003)
Handbook of Chemoinformatics from Data to Knowledge
, pp. 1789-1811
-
-
Rost, B.1
Liu, J.2
Przybylski, D.3
Nair, R.4
Wrzeszczynski, K.5
Bigelow, H.6
Ofran, Y.7
-
20
-
-
0036681397
-
Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory
-
R.E. Steward and J.M. Thornton, "Prediction of Strand Pairing in Antiparallel and Parallel Beta-Sheets Using Information Theory," Proteins: Structure, Function, and Genetics, vol. 48, pp. 178-191, 2002.
-
(2002)
Proteins: Structure, Function, and Genetics
, vol.48
, pp. 178-191
-
-
Steward, R.E.1
Thornton, J.M.2
-
21
-
-
0032438987
-
Hidden markov models for detecting remote protein homologies
-
K. Karplus, C. Barrett, and R. Hughey, "Hidden Markov Models for Detecting Remote Protein Homologies," Bioinformatics, vol. 14, pp. 846-856, 1998.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
22
-
-
0034564269
-
Matching protein/3-sheet partners by feedforward and recurrent neural networs
-
P. Baldi, G Pollastri, C.A.F. Andersen, and S. Brunak, "Matching Protein/3-Sheet Partners by Feedforward and Recurrent Neural Networs," Proc. 2000 Conf. Intelligent Systems for Molecular Biology (ISMB '00), pp. 25-36, 2000.
-
(2000)
Proc. 2000 Conf. Intelligent Systems for Molecular Biology (ISMB '00)
, pp. 25-36
-
-
Baldi, P.1
Pollastri, G.2
Andersen, C.A.F.3
Brunak, S.4
-
23
-
-
0041719954
-
Prediction of contact maps by giohmms and recurrent neural networks using lateral propagation from all four cardinal corners
-
G Pollastri and P. Baldi, "Prediction of Contact Maps by GIOHMMs and Recurrent Neural Networks Using Lateral Propagation from All Four Cardinal Corners," Bioinformatics, vol. 18, pp. S62-S70, 2002.
-
(2002)
Bioinformatics
, vol.18
-
-
Pollastri, G.1
Baldi, P.2
-
24
-
-
4043170491
-
Protein contact prediction using patterns of correlation
-
N. Hamilton, K. Burrage, M. Ragan, and T. Huber, "Protein Contact Prediction Using Patterns of Correlation," Proteins, vol. 56, pp. 679-684, 2004.
-
(2004)
Proteins
, vol.56
, pp. 679-684
-
-
Hamilton, N.1
Burrage, K.2
Ragan, M.3
Huber, T.4
-
25
-
-
24744453057
-
Striped sheets and protein contact prediction
-
R. MacCallum, "Striped Sheets and Protein Contact Prediction," Bioinformatics, vol. 20, pp. i224-i231, 2004.
-
(2004)
Bioinformatics
, vol.20
-
-
MacCallum, R.1
-
26
-
-
84860507958
-
Three-stage prediction of protein/3-sheets by neural networks, alignments and graph algorithms
-
J. Cheng and P. Baldi, "Three-Stage Prediction of Protein/3-Sheets by Neural Networks, Alignments and Graph Algorithms," Bioinformatics, vol. 21, pp. i75-i84, 2005.
-
(2005)
Bioinformatics
, vol.21
-
-
Cheng, J.1
Baldi, P.2
-
27
-
-
23144465987
-
SCRATCH: A protein structure and structural feature prediction server
-
J. Cheng, A. Randall, M. Sweredoski, and P. Baldi, "SCRATCH: A Protein Structure and Structural Feature Prediction Server," Nucleic Acids Research, vol. 33, pp. w72-w76, 2005.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Cheng, J.1
Randall, A.2
Sweredoski, M.3
Baldi, P.4
-
28
-
-
21444454088
-
PROFcon: Novel prediction of long-range contacts
-
M. Punta and B. Rost, "PROFcon: Novel Prediction of Long-Range Contacts," Bioinformatics, vol. 21, pp. 2960-2968, 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 2960-2968
-
-
Punta, M.1
Rost, B.2
-
29
-
-
33745610096
-
A two-stage approach for improved prediction of residue contact maps
-
article no. 180
-
A. Vullo, I. Walsh, and G Pollastri, "A Two-Stage Approach for Improved Prediction of Residue Contact Maps," BMC Bioinformatics, vol. 7, article no. 180, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Vullo, A.1
Walsh, I.2
Pollastri, G.3
-
30
-
-
33749139123
-
Distill: A suite of web servers for the prediction of one-, two-and three-dimensional structural features of proteins
-
article no. 402
-
D. Bau, A. Martin, C. Mooney, A. Vullo, I. Walsh, and G Pollastri, "Distill: A Suite of Web Servers for the Prediction of One-, Two-and Three-Dimensional Structural Features of Proteins," BMC Bioinformatics, vol. 7, article no. 402, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
-
-
Bau, D.1
Martin, A.2
Mooney, C.3
Vullo, A.4
Walsh, I.5
Pollastri, G.6
-
31
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
article no. 113
-
J. Cheng and P. Baldi, "Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set," BMC Bioinformatics, vol. 8, article no. 113, 2007.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Cheng, J.1
Baldi, P.2
-
32
-
-
0035910068
-
BETAWRAP: Successful prediction of parallel/3-helices from primary sequence reveals an association with many pathogens
-
P. Bradley, L. Cowen, M. Menke, J. King, and B. Berger, "BETAWRAP: Successful Prediction of Parallel/3-Helices from Primary Sequence Reveals an Association with Many Pathogens," Proc. Nat'l Academy of Science USA, vol. 98, pp. 14819-14824, 2001.
-
(2001)
Proc. Nat'l Academy of Science USA
, vol.98
, pp. 14819-14824
-
-
Bradley, P.1
Cowen, L.2
Menke, M.3
King, J.4
Berger, B.5
-
33
-
-
33748278030
-
Predicting transmembrane/3-barrels and interstrand residue interactions from sequence
-
J. Waldispuhl, B. Berger, P. Clote, and J.M. Steyaert, "Predicting Transmembrane/3-Barrels and Interstrand Residue Interactions from Sequence," PROTEINS: Structure, Function, and Bioinformatics, vol. 65, pp. 61-74, 2006.
-
(2006)
PROTEINS: Structure, Function, and Bioinformatics
, vol.65
, pp. 61-74
-
-
Waldispuhl, J.1
Berger, B.2
Clote, P.3
Steyaert, J.M.4
-
34
-
-
39149140433
-
TMBpro: Secondary structure,/3-contact and tertiary structure prediction of transmembrane/3-barrel proteins
-
A. Randall, J. Cheng, M. Sweredoski, and P. Baldi, "TMBpro: Secondary Structure,/3-Contact and Tertiary Structure Prediction of Transmembrane/3-Barrel Proteins," Bioinformatics, vol. 24, pp. 513-520, 2008.
-
(2008)
Bioinformatics
, vol.24
, pp. 513-520
-
-
Randall, A.1
Cheng, J.2
Sweredoski, M.3
Baldi, P.4
-
35
-
-
37249010577
-
Bringing folding pathways into strand pairing prediction
-
J. Jeong, P. Berman, and T. Przytycka, "Bringing Folding Pathways into Strand Pairing Prediction," Proc. Workshop Algorithms in Bioinformatics (WABI), pp. 38-49, 2007.
-
(2007)
Proc. Workshop Algorithms in Bioinformatics (WABI)
, pp. 38-49
-
-
Jeong, J.1
Berman, P.2
Przytycka, T.3
-
37
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
-
W. Kabsch and C Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features," Biopolymers, vol. 22, pp. 2577-2637, 1983.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
39
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
S.B. Needleman and CD. Wunsch, "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins," J. Molecular Biology, vol. 48, pp. 443-453, 1970.
-
(1970)
J. Molecular Biology
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
40
-
-
79551666287
-
An improved algorithm for matching biological sequences
-
O. Gotoh, "An Improved Algorithm for Matching Biological Sequences," J. Molecular Biology, vol. 264, pp. 823-838, 1982.
-
(1982)
J. Molecular Biology
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
42
-
-
21244471882
-
-
Cambridge Univ. Press
-
R. Durbin, S. Eddy, A. Krogh, and G Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge Univ. Press, 1998.
-
(1998)
Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
Sequence Analysis, B.5
-
44
-
-
79551664753
-
-
"Dunbrack Lab," http://dunbrack.fcc.edu, 2008.
-
(2008)
Dunbrack Lab
-
-
-
46
-
-
79551672150
-
-
"BetaSheet916 Set," http://www.ics.uci.edu/~baldig/betasheet- data.html, 2009.
-
(2009)
BetaSheet916 Set
-
-
-
47
-
-
79551675343
-
-
"NCBI BLAST Downloads," http://www.ncbi.nlm.nih.gov/BLAST/ download.shtml,
-
(2009)
NCBI BLAST Downloads
-
-
|