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Publication index
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Sorted by year
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Sorted by category
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Collected abstracts |
Clustering proteins:
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Automatic target selection for structural genomics on eukaryotes
J Liu, H Hegyi, TB Acton, GT Montelione and B Rost
2004
Proteins. 2004 Aug 1;56(2):188-200.
(abstr, www, pdf)
|
CHOP proteins into structural domains
J Liu and B Rost
2004
Proteins, 55, 678-686
(abstr, www, pdf)
|
The Protein Target List of the Northeast Structural Genomics Consortium
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost and GT Montelione
2004
Proteins. 2004 Aug 1;56(2):181-187.
(abstr, www, pdf)
|
Target space for structural genomics revisited
J Liu and B Rost
2002
Bioinformatics, 18, 922-933
(abstr, www, pdf)
|
Genomics predictions:
|
Distinguishing protein-coding from non-coding RNAs through support vector machines.
Liu J, Gough J, Rost B.
2006
PLoS Genet. 2006 Apr;2(4):e29. Epub 2006 Apr 28.
(abstr, www, pdf)
|
Alignment methods:
|
Improving fold recognition without folds
D Przybylski and B Rost
2004
JMB, 2004 Jul30;341(1):255-69
(abstr, www, pdf)
|
Alignments grow, secondary structure prediction improves
D Przybylski and B Rost
2002
Proteins, 46, 197-205
(abstr, www, pdf)
|
Twilight zone of protein sequence alignments
B Rost
1999
Protein Engineering, 12, 85-94
(abstr, www, pdf)
|
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
B Rost
1995
Third International Conference on Intelligent Systems for Molecular Biology, , 314-321
(abstr, www, pdf)
|
Sub-cellular localization:
|
Annotating proteins from Endoplasmic Reticulum and Golgi apparatus in eukaryotic proteomes
KO Wrzeszczynski and B Rost
2004
Cellular and Molecular Life Sciences, volxx, submitted_pages_xx
(abstr, www, pdf)
|
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets
R Nair and B Rost
2004
Nucl. Acids. Res. 2004 32(Web Server Issue): W517-W521.
(abstr, www, pdf)
|
NLSdb: database of nuclear localization signals
R Nair, P Carter and B Rost
2003
Nucl Acid Res, 322, 397-399
(abstr, www, pdf)
|
LOC3D: annotate sub-cellular localization for protein structures
R Nair and B Rost
2003
Nucl Acids Res, 31, 3337-3340
(abstr, www, pdf)
|
Better prediction of sub-cellular localization through evolution and structure
R Nair and B Rost
2003
Proteins, 53, 917-930
(abstr, www, pdf)
|
Sequence conserved for sub-cellular localization
R Nair and B Rost
2002
Protein Science, 11, 2836-2847
(abstr, www, pdf)
|
Inferring sub-cellular localization through automated lexical analysis
R Nair and B Rost
2002
Bioinformatics, 18:Suppl 1, S78-S86
(abstr, www, pdf)
|
Prediction services:
|
PROFbval: predict flexible and rigid residues in proteins.
Schlessinger A, Yachdav G, Rost B.
2006
Bioinformatics. 2006 Apr 1;22(7):891-3. Epub 2006 Feb 2.
(abstr, www, pdf)
|
CHOP: parsing proteins into structural domains
J Liu and B Rost
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W569-W571.
(abstr, www, pdf)
|
The PredictProtein server
B Rost, G Yachdav and J Liu
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W321-W326.
(abstr, www, pdf)
|
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets
R Nair and B Rost
2004
Nucl. Acids. Res. 2004 32(Web Server Issue): W517-W521.
(abstr, www, pdf)
|
Static benchmarking of membrane helix predictions
A Kernytsky and B Rost
2003
Nucl Acids Res, 31, 3642-3644
(abstr, www, pdf)
|
DSSPcont: continuous secondary structure assignments for proteins
P Carter, CAF Andersen and B Rost
2003
Nucl Acids Res, 31, 3293-3295
(abstr, www, pdf)
|
LOC3D: annotate sub-cellular localization for protein structures
R Nair and B Rost
2003
Nucl Acids Res, 31, 3337-3340
(abstr, www, pdf)
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
META-PP: single crucial to prediction servers
VA Eyrich and B Rost
2003
Nucl Acids Res, 31, 3308-3310
(abstr, www, pdf)
|
NORSp: predictions of long regions without regular secondary structure
J Liu and B Rost
2003
Nucl Acids Res, 31, 3833-3835
(abstr, www, pdf)
|
CAFASP3 in the spotlight of EVA
VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost
2003
Proteins, 53 S6, 548-560
(abstr, www, pdf)
|
UniqueProt: creating sequence-unique protein data sets
S Mika and B Rost
2003
Nucl Acids Res, 31, 3789-3791
(abstr, www, pdf)
|
EVA: evaluation of protein structure prediction servers
IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost
2003
Nucl Acids Res, 31, 3311-3315
(abstr, www, pdf)
|
PHD - an automatic server for protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
CABIOS, 10, 53-60
(abstr, www, pdf)
|
Solvent accessibility:
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
Alignments grow, secondary structure prediction improves
D Przybylski and B Rost
2002
Proteins, 46, 197-205
(abstr, www, pdf)
|
Short yeast ORFs: expressed protein or not?
B Rost
1999
Preprint CUBIC, 1999_1
(abstr, www, pdf)
|
Adaptation of protein surfaces to subcellular location
MA Andrade, SI O'Donoghue and B Rost
1998
Journal of Molecular Biology, 276, 517-525
(abstr, www, pdf)
|
Better 1D predictions by experts with machines. Proteins, Suppl
B Rost
1997
1, 192-197
(abstr, www, pdf)
|
PHD: predicting one-dimensional protein structure by profile based neural networks
B Rost and A Valencia
1996
Current Opinion in Biotechnology, 7, 457-461
(abstr, www, pdf)
|
Progress of 1D protein structure prediction at last
B Rost and C Sander
1995
Proteins, 23, 295-300
(abstr, www, pdf)
|
Conservation and prediction of solvent accessibility in protein families
B Rost and C Sander
1994
Proteins, 20, 216-226
(abstr, www, pdf)
|
Protein Structure:
|
PROFbval: predict flexible and rigid residues in proteins.
Schlessinger A, Yachdav G, Rost B.
2006
Bioinformatics. 2006 Apr 1;22(7):891-3. Epub 2006 Feb 2.
(abstr, www, pdf)
|
Threading (remote homology):
|
Improving fold recognition without folds
D Przybylski and B Rost
2004
JMB, 2004 Jul30;341(1):255-69
(abstr, www, pdf)
|
CAFASP3 in the spotlight of EVA
VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost
2003
Proteins, 53 S6, 548-560
(abstr, www, pdf)
|
EVA: evaluation of protein structure prediction servers
IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost
2003
Nucl Acids Res, 31, 3311-3315
(abstr, www, pdf)
|
EVA: continuous automatic evaluation of protein structure prediction servers
VA Eyrich, MA Marti-Renom, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, and B. Rost
2001
Bioinformatics, 17, 1242-1243
(abstr, www, pdf)
|
A platform for integrating threading results with protein family analyses
F Pazos, B Rost and A Valencia
1999
Bioinformatics, 15, 1062-1063
(abstr, www, pdf)
|
Effective use of sequence correlation and conservation in fold recognition
O Olmea, B Rost and A Valencia
1999
Journal of Molecular Biology, 293, 1221-1239
(abstr, www, pdf)
|
Protein fold recognition by prediction-based threading
B Rost, R Schneider and C Sander
1997
Journal of Molecular Biology, 270, 471-480
(abstr, www, pdf)
|
Update on protein structure prediction: results of the 1995 IRBM workshop
T Hubbard, A Tramontano, G Barton, D Jones, M Sippl, A Valencia, A Lesk, J Moult, B Rost, C Sander, R Schneider, A Lahm, R Leplae, C Buta , M Eisenstein, O Fjellström, H Floeckner, JG Grossmann, J Hansen, M Helmer-Citterich, FS Joergensen, A Marchler-Bauer, J Osuna, J Park, A Reinhardt, L Ribas de Pouplana, A Rojo-Dominguez, V Saudek, J Sinclair, S Sturrock, C Venclovas and C Vinals
1996
Folding & Design, 1, R55-
(abstr, www, pdf)
|
Fitting 1-D predictions into 3-D structures.
B Rost
1995
in: 'Protein folds: a distance based approach' (eds H Bohr and S Brunak), , 132-151
(abstr, www, pdf)
|
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
B Rost
1995
Third International Conference on Intelligent Systems for Molecular Biology, , 314-321
(abstr, www, pdf)
|
Reviews:
|
How to use protein 1D structure predicted by PROFphd.
B Rost
2004
in: 'Proteomics Handbook' (ed JM Walker), Methods in Molecular Biology, Humana Press, submitted_pages_xx
(abstr, www, pdf)
|
Annotating protein function through lexical analysis
R Nair and B Rost
2004
AI Magazine, 25, 45-56
(abstr, www, pdf)
|
Cataloguing proteins in cell cycle control.
KO Wrzeszczynski and B Rost
2003
in: 'Cell cycle checkpoint control protocols' (ed H Liebermann), Totowa: Humana Press, 219-233
(abstr, www, pdf)
|
Automatic prediction of protein function
B Rost, J Liu, R Nair, KO Wrzeszczynski and Y Ofran
2003
Cellular Molecular Life Sciences, 12, 2637-2650
(abstr, www, pdf)
|
Neural networks predict protein structure: hype or hit?.
B Rost
2003
in: 'Artificial intelligence and heuristic methods for bioinformatics' (ed P Frasconi), Amsterdam: IOS Press, 34-50
(abstr, www, pdf)
|
Prediction of protein structure through evolution.
B Rost, J Liu, D Przybylski, R Nair, KO Wrzeszczynski, H Bigelow and Y Ofran
2003
in: 'Handbook of Chemoinformatics - From Data to Knowledge' (eds J Gasteiger & T Engel), Weinheim: Wiley-VCH, 1789-1811
(abstr, www, pdf)
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Prediction In 1D: secondary structure, membrane helices, and accessibility.
B Rost
2003
in: 'Structural Bioinformatics' (eds P Bourne and H Weissig), New York: Wiley, 557-585
(abstr, www, pdf)
|
Secondary structure assignment.
CAF Andersen and B Rost
2003
in: 'Structural Bioinformatics' (eds P Bourne and H Weissig), New York: Wiley, 339-361
(abstr, www, pdf)
|
Rising accuracy of protein secondary structure prediction.
B Rost
2003
in: 'Protein structure determination, analysis, and modeling for drug discovery' (ed D Chasman), New York: Dekker, 207-249
(abstr, www, pdf)
|
Domains, motifs, and clusters in the protein universe
J Liu and B Rost
2003
Curr Opinion Chem Biol, 7, 5-11
(abstr, www, pdf)
|
Did evolution leap to create the protein universe?
B Rost
2002
Curr Opin Struc Biol, 12, 409-416
(abstr, www, pdf)
|
State-of-the-art in membrane protein prediction
CP Chen and B Rost
2002
Applied Bioinformatics, 1, 21-35
(abstr, www, pdf)
|
Protein secondary structure prediction continues to rise
B Rost
2001
J Structural Biology, 134, 204-218
(abstr, www, pdf)
|
EVA: large-scale analysis of secondary structure prediction
B Rost and VE Eyrich
2001
Proteins, 45:S5, S192-199
(abstr, www, pdf)
|
Third generation prediction of secondary structure.
B Rost and C Sander
2000
in: 'Protein structure prediction: Methods and Protocols' (ed. D Webster), Totowa, NJ: Humana Press, 71-95
(abstr, www, pdf)
|
Marrying structure and genomics
B Rost
1998
Structure, 6, 259-263
(abstr, www, pdf)
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Protein structure prediction in 1D, 2D, and 3D.
B Rost
1998
in: 'The Encyclopaedia of Computational Chemistry' (eds PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III and PR Schreiner), 3, 2242-2255
(abstr, www, pdf)
|
Learning from evolution to predict protein structure
B Rost
1997
BCEC97: Bio-Computing and Emergent Computation, , 87-101
(abstr, www, pdf)
|
Sisyphus and prediction of protein structure
B Rost and SI O'Donoghue
1997
Computer Applications in Biological Science, 13, 345-356
(abstr, www, pdf)
|
NN which predicts protein secondary structure.
B Rost
1997
in: 'Handbook of Neural Computation' (eds E Fiesler and R Beale), , G4.1
(abstr, www, pdf)
|
Bridging the protein sequence-structure gap by structure predictions
B Rost and C Sander
1996
Annual Review of Biophysics and Biomolecular Structure, 25, 113-136
(abstr, www, pdf)
|
Pitfalls of protein sequence analysis
B Rost and A Valencia
1996
Current Opinion in Biotechnology, 7, 457-461
(abstr, www, pdf)
|
Protein structure prediction by neural networks.
B Rost and C Sander
1995
in: 'The handbook of brain theory and neural networks' (eds M Arbib), , 772-775
(abstr, www, pdf)
|
Structure prediction of proteins - where are we now?
B Rost and C Sander
1994
Current Opinion in Biotechnology, 5, 372-380
(abstr, www, pdf)
|
Neural networks in chemistry
B Rost and G Vriend
1993
CDA News, 8, 24-27
(abstr, www, pdf)
|
Progress in protein structure prediction?
B Rost, C Sander and R Schneider
1993
TIBS, 18, 120-123
(abstr, www, pdf)
|
Protein structure:
|
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Bigelow H, Rost B.
2006
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W186-8.
(abstr, www, pdf)
|
Protein flexibility and rigidity predicted from sequence
A Schlessinger and B Rost
2005
Proteins, 2005, in press
(abstr, www, pdf)
|
CASP6 assessment of contact prediction
O. Grana, D. Baker, R.M. MacCallum, J. Meiler, M. Punta, B. Rost, M. L. Tress, and A. Valencia
2005
Proteins 2005 61 Suppl 7:214-24
(abstr, www, pdf)
|
Epitome: Database of structure-inferred antigenic epitopes
A Schlessinger, Y Ofran, G Yachdav and B Rost
2005
NAR (Database Issue) 2005, in press.
(abstr, www, pdf)
|
Protein folding rates estimated from contact predictions
M Punta and B Rost
2005
Journal of Molecular Biology Volume 348 (3), 507-512
(abstr, www, pdf)
|
PROFcon: novel prediction of long-range contacts
M Punta and B Rost
2005
Bioinformatics, 2005, Jul 1;21(13):2960-8
(abstr, www, pdf)
|
Sequence-based prediction of protein domains
J Liu and B Rost
2004
Nucleic Acids Res. 2004 Jul 07;32(12):3522-30. Print 2004
(abstr, www, pdf)
|
CHOP: parsing proteins into structural domains
J Liu and B Rost
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W569-W571.
(abstr, www, pdf)
|
Improving fold recognition without folds
D Przybylski and B Rost
2004
JMB, 2004 Jul30;341(1):255-69
(abstr, www, pdf)
|
Predicting transmembrane beta-barrels for entire proteomes
H Bigelow, D Petrey, J Liu, D Przybylski and B Rost
2004
NAR, 32, 2566-2577
(abstr, www, pdf)
|
The PredictProtein server
B Rost, G Yachdav and J Liu
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W321-W326.
(abstr, www, pdf)
|
DSSPcont: continuous secondary structure assignments for proteins
P Carter, CAF Andersen and B Rost
2003
Nucl Acids Res, 31, 3293-3295
(abstr, www, pdf)
|
LOC3D: annotate sub-cellular localization for protein structures
R Nair and B Rost
2003
Nucl Acids Res, 31, 3337-3340
(abstr, www, pdf)
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii
JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton and GT Montelione
2003
Prot Sci, 12, 2823-2830
(abstr, www, pdf)
|
NORSp: predictions of long regions without regular secondary structure
J Liu and B Rost
2003
Nucl Acids Res, 31, 3833-3835
(abstr, www, pdf)
|
Transmembrane domains in the functions of Fc receptors
R Zidovetzki, B Rost, DL Armstrong and I Pecht
2003
J Biophys Chem, 15, 555-575
(abstr, www, pdf)
|
CAFASP3 in the spotlight of EVA
VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost
2003
Proteins, 53 S6, 548-560
(abstr, www, pdf)
|
Better prediction of sub-cellular localization through evolution and structure
R Nair and B Rost
2003
Proteins, 53, 917-930
(abstr, www, pdf)
|
EVA: evaluation of protein structure prediction servers
IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost
2003
Nucl Acids Res, 31, 3311-3315
(abstr, www, pdf)
|
Loopy proteins appear conserved in evolution
J Liu, H Tan and B Rost
2002
J Mol Biol, 322, 53-64
(abstr, www, pdf)
|
Continuum secondary structure captures protein flexibility
CAF Andersen, AG Palmer, S Brunak and B Rost
2002
Structure, 10, 175-185
(abstr, www, pdf)
|
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
G Pollastri, D Przybylski, B Rost and P Baldi
2002
Proteins, 47, 228-235
(abstr, www, pdf)
|
Reliability of assessment of protein structure prediction methods
MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost and A Sali
2002
Structure, 10, 435-440
(abstr, www, pdf)
|
Alignments grow, secondary structure prediction improves
D Przybylski and B Rost
2002
Proteins, 46, 197-205
(abstr, www, pdf)
|
EVA: continuous automatic evaluation of protein structure prediction servers
VA Eyrich, MA Marti-Renom, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali, and B. Rost
2001
Bioinformatics, 17, 1242-1243
(abstr, www, pdf)
|
Cafasp2: The second critical assessment of fully automated structure prediction methods
D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz and RLJ Dunbrack
2001
Proteins, 45 Suppl 5, S171-183
(abstr, www, pdf)
|
A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment
A Zemla, C Venclovas, K Fidelis and B Rost
1999
Proteins, 34, 220-223
(abstr, www, pdf)
|
Short yeast ORFs: expressed protein or not?
B Rost
1999
Preprint CUBIC, 1999_1
(abstr, www, pdf)
|
Adaptation of protein surfaces to subcellular location
MA Andrade, SI O'Donoghue and B Rost
1998
Journal of Molecular Biology, 276, 517-525
(abstr, www, pdf)
|
Protein fold recognition by prediction-based threading
B Rost, R Schneider and C Sander
1997
Journal of Molecular Biology, 270, 471-480
(abstr, www, pdf)
|
Better 1D predictions by experts with machines. Proteins, Suppl
B Rost
1997
1, 192-197
(abstr, www, pdf)
|
Protein structures sustain evolutionary drift
B Rost
1997
Folding & Design, 2, S19-S24
(abstr, www, pdf)
|
PHD: predicting one-dimensional protein structure by profile based neural networks
B Rost and A Valencia
1996
Current Opinion in Biotechnology, 7, 457-461
(abstr, www, pdf)
|
Refining neural network predictions for helical transmembrane proteins by dynamic programming
B Rost, R Casadio and P Fariselli
1996
Fourth International Conference on Intelligent Systems for Molecular Biology, , 192-200
(abstr, www, pdf)
|
Topology prediction for helical transmembrane proteins at 86% accuracy
B Rost, R Casadio and P Fariselli
1996
Protein Science, 5, 1704-1718
(abstr, www, pdf)
|
Progress of 1D protein structure prediction at last
B Rost and C Sander
1995
Proteins, 23, 295-300
(abstr, www, pdf)
|
Prediction of helical transmembrane segments at 95% accuracy
B Rost, R Casadio, P Fariselli and C Sander
1995
Protein Science, 4, 521-533
(abstr, www, pdf)
|
Fitting 1-D predictions into 3-D structures.
B Rost
1995
in: 'Protein folds: a distance based approach' (eds H Bohr and S Brunak), , 132-151
(abstr, www, pdf)
|
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
B Rost
1995
Third International Conference on Intelligent Systems for Molecular Biology, , 314-321
(abstr, www, pdf)
|
Conservation and prediction of solvent accessibility in protein families
B Rost and C Sander
1994
Proteins, 20, 216-226
(abstr, www, pdf)
|
1D secondary structure prediction through evolutionary profiles.
B Rost and C Sander
1994
in: 'Protein Structure by Distance Analysis' (eds H Bohr and S Brunak), , 257-276
(abstr, www, pdf)
|
Redefining the goals of protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
Journal of Molecular Biology, 235, 13-26
(abstr, www, pdf)
|
Evolution and neural networks - protein secondary structure prediction above 71% accuracy
B Rost, C Sander and R Schneider
1994
27th Hawaii International Conference on System Sciences, 5, 385-394
(abstr, www, pdf)
|
Combining evolutionary information and neural networks to predict protein secondary structure
B Rost and C Sander
1994
Proteins, 19, 55-72
(abstr, www, pdf)
|
Data based modeling of proteins
L Holm, B Rost, C Sander, R Schneider and G Vriend
1994
Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, , 277-296
(abstr, www, pdf)
|
PHD - an automatic server for protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
CABIOS, 10, 53-60
(abstr, www, pdf)
|
Secondary structure prediction of all-helical proteins in two states
B Rost and C Sander
1993
Protein Engineering, 6, 831-836
(abstr, www, pdf)
|
Prediction of protein secondary structure at better than 70% accuracy
B Rost and C Sander
1993
Journal of Molecular Biology, 232, 584-599
(abstr, www, pdf)
|
Improved prediction of protein secondary structure by use of sequence profiles and neural networks
B Rost and C Sander
1993
Proceedings of the National Academy of Sciences, 90, 7558-7562
(abstr, www, pdf)
|
Jury returns on structure prediction
B Rost and C Sander
1992
Nature, 360, 540
(abstr, www, pdf)
|
Exercising multi-layered networks on protein secondary structure
B Rost and C Sander
1992
Neural Networks: From Biology to High Energy Physics, 3, 209-220
(abstr, www, pdf)
|
Transmembrane segments:
|
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Bigelow H, Rost B.
2006
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W186-8.
(abstr, www, pdf)
|
Predicting transmembrane beta-barrels for entire proteomes
H Bigelow, D Petrey, J Liu, D Przybylski and B Rost
2004
NAR, 32, 2566-2577
(abstr, www, pdf)
|
Static benchmarking of membrane helix predictions
A Kernytsky and B Rost
2003
Nucl Acids Res, 31, 3642-3644
(abstr, www, pdf)
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
Transmembrane domains in the functions of Fc receptors
R Zidovetzki, B Rost, DL Armstrong and I Pecht
2003
J Biophys Chem, 15, 555-575
(abstr, www, pdf)
|
State-of-the-art in membrane protein prediction
CP Chen and B Rost
2002
Applied Bioinformatics, 1, 21-35
(abstr, www, pdf)
|
Transmembrane helix predictions revisited
CP Chen, A Kernytsky and B Rost
2002
Protein Science, 11, 2774-2791
(abstr, www, pdf)
|
Long membrane helices and short loops predicted less accurately
CP Chen and B Rost
2002
Protein Science, 11, 2766-2773
(abstr, www, pdf)
|
Comparing function and structure between entire proteomes
J Liu and B Rost
2001
Protein Science, 10, 1970-1979
(abstr, www, pdf)
|
The role of transmembrane domains in the functions of B- and T-cell receptors
R Zidovetzki, B Rost and I Pecht
1998
Immunology Letters, 64, 97-107
(abstr, www, pdf)
|
PHD: predicting one-dimensional protein structure by profile based neural networks
B Rost and A Valencia
1996
Current Opinion in Biotechnology, 7, 457-461
(abstr, www, pdf)
|
Refining neural network predictions for helical transmembrane proteins by dynamic programming
B Rost, R Casadio and P Fariselli
1996
Fourth International Conference on Intelligent Systems for Molecular Biology, , 192-200
(abstr, www, pdf)
|
Topology prediction for helical transmembrane proteins at 86% accuracy
B Rost, R Casadio and P Fariselli
1996
Protein Science, 5, 1704-1718
(abstr, www, pdf)
|
Prediction of helical transmembrane segments at 95% accuracy
B Rost, R Casadio, P Fariselli and C Sander
1995
Protein Science, 4, 521-533
(abstr, www, pdf)
|
Protein-protein interaction:
|
Protein-protein interactions more conserved within species than across species.
Mika S, Rost B.
2006
PLoS Comput Biol. 2006 Jul 21;2(7):e79. Epub 2006 May 18.
(abstr, www, pdf)
|
Analysing six types of protein-protein interfaces
Y Ofran and B Rost
2003
J Mol Biol, 325, 377-387
(abstr, www, pdf)
|
Local sequence information can predict protein-protein interaction sites
Y Ofran and B Rost
2003
FEBS Let, 544, 236-239
(abstr, www, pdf)
|
Evaluation of prediction methods:
|
Static benchmarking of membrane helix predictions
A Kernytsky and B Rost
2003
Nucl Acids Res, 31, 3642-3644
(abstr, www, pdf)
|
CAFASP3 in the spotlight of EVA
VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost
2003
Proteins, 53 S6, 548-560
(abstr, www, pdf)
|
EVA: evaluation of protein structure prediction servers
IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost
2003
Nucl Acids Res, 31, 3311-3315
(abstr, www, pdf)
|
Transmembrane helix predictions revisited
CP Chen, A Kernytsky and B Rost
2002
Protein Science, 11, 2774-2791
(abstr, www, pdf)
|
Enzyme function less conserved than anticipated
B Rost
2002
J Mol Biol, 318, 595-608
(abstr, www, pdf)
|
Reliability of assessment of protein structure prediction methods
MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost and A Sali
2002
Structure, 10, 435-440
(abstr, www, pdf)
|
Long membrane helices and short loops predicted less accurately
CP Chen and B Rost
2002
Protein Science, 11, 2766-2773
(abstr, www, pdf)
|
A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment
A Zemla, C Venclovas, K Fidelis and B Rost
1999
Proteins, 34, 220-223
(abstr, www, pdf)
|
Protein fold recognition by prediction-based threading
B Rost, R Schneider and C Sander
1997
Journal of Molecular Biology, 270, 471-480
(abstr, www, pdf)
|
Progress of 1D protein structure prediction at last
B Rost and C Sander
1995
Proteins, 23, 295-300
(abstr, www, pdf)
|
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
B Rost
1995
Third International Conference on Intelligent Systems for Molecular Biology, , 314-321
(abstr, www, pdf)
|
Redefining the goals of protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
Journal of Molecular Biology, 235, 13-26
(abstr, www, pdf)
|
Structural genomics:
|
Protein flexibility and rigidity predicted from sequence
A Schlessinger and B Rost
2005
Proteins, 2005, in press
(abstr, www, pdf)
|
Sequence-based prediction of protein domains
J Liu and B Rost
2004
Nucleic Acids Res. 2004 Jul 07;32(12):3522-30. Print 2004
(abstr, www, pdf)
|
Automatic target selection for structural genomics on eukaryotes
J Liu, H Hegyi, TB Acton, GT Montelione and B Rost
2004
Proteins. 2004 Aug 1;56(2):188-200.
(abstr, www, pdf)
|
CHOP proteins into structural domains
J Liu and B Rost
2004
Proteins, 55, 678-686
(abstr, www, pdf)
|
CHOP: parsing proteins into structural domains
J Liu and B Rost
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W569-W571.
(abstr, www, pdf)
|
The Protein Target List of the Northeast Structural Genomics Consortium
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost and GT Montelione
2004
Proteins. 2004 Aug 1;56(2):181-187.
(abstr, www, pdf)
|
The PredictProtein server
B Rost, G Yachdav and J Liu
2004
Nucleic Acids Res. 2004 Jul 1;32(Web Server Issue):W321-W326.
(abstr, www, pdf)
|
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets
R Nair and B Rost
2004
Nucl. Acids. Res. 2004 32(Web Server Issue): W517-W521.
(abstr, www, pdf)
|
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii
JM Aramini, YJ Huang, JR Cort, S Goldsmith-Fischman, R Xiao, LY Shih, CK Ho, J Liu, B Rost, B Honig, MA Kennedy, TB Acton and GT Montelione
2003
Prot Sci, 12, 2823-2830
(abstr, www, pdf)
|
PEP: Predictions for Entire Proteomes
P Carter, J Liu and B Rost
2003
Nucl Acid Res, 31, 410-413
(abstr, www, pdf)
|
Loopy proteins appear conserved in evolution
J Liu, H Tan and B Rost
2002
J Mol Biol, 322, 53-64
(abstr, www, pdf)
|
Enzyme function less conserved than anticipated
B Rost
2002
J Mol Biol, 318, 595-608
(abstr, www, pdf)
|
Target space for structural genomics revisited
J Liu and B Rost
2002
Bioinformatics, 18, 922-933
(abstr, www, pdf)
|
Sequence analysis:
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
Analysing six types of protein-protein interfaces
Y Ofran and B Rost
2003
J Mol Biol, 325, 377-387
(abstr, www, pdf)
|
META-PP: single crucial to prediction servers
VA Eyrich and B Rost
2003
Nucl Acids Res, 31, 3308-3310
(abstr, www, pdf)
|
UniqueProt: creating sequence-unique protein data sets
S Mika and B Rost
2003
Nucl Acids Res, 31, 3789-3791
(abstr, www, pdf)
|
Loopy proteins appear conserved in evolution
J Liu, H Tan and B Rost
2002
J Mol Biol, 322, 53-64
(abstr, www, pdf)
|
Sequence conserved for sub-cellular localization
R Nair and B Rost
2002
Protein Science, 11, 2836-2847
(abstr, www, pdf)
|
Comparing function and structure between entire proteomes
J Liu and B Rost
2001
Protein Science, 10, 1970-1979
(abstr, www, pdf)
|
Twilight zone of protein sequence alignments
B Rost
1999
Protein Engineering, 12, 85-94
(abstr, www, pdf)
|
The role of transmembrane domains in the functions of B- and T-cell receptors
R Zidovetzki, B Rost and I Pecht
1998
Immunology Letters, 64, 97-107
(abstr, www, pdf)
|
Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure
T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann and J Murken
1993
Nature Genetics, 5, 376-380
(abstr, www, pdf)
|
Proteomics predictions:
|
Protein flexibility and rigidity predicted from sequence
A Schlessinger and B Rost
2005
Proteins, 2005, in press
(abstr, www, pdf)
|
The Protein Target List of the Northeast Structural Genomics Consortium
Z Wunderlich, TB Acton, J Liu, G Kornhaber, J Everett, P Carter, N Lan, N Echols, M Gerstein, B Rost and GT Montelione
2004
Proteins. 2004 Aug 1;56(2):181-187.
(abstr, www, pdf)
|
NLSdb: database of nuclear localization signals
R Nair, P Carter and B Rost
2003
Nucl Acid Res, 322, 397-399
(abstr, www, pdf)
|
PEP: Predictions for Entire Proteomes
P Carter, J Liu and B Rost
2003
Nucl Acid Res, 31, 410-413
(abstr, www, pdf)
|
Loopy proteins appear conserved in evolution
J Liu, H Tan and B Rost
2002
J Mol Biol, 322, 53-64
(abstr, www, pdf)
|
Sequence conserved for sub-cellular localization
R Nair and B Rost
2002
Protein Science, 11, 2836-2847
(abstr, www, pdf)
|
Target space for structural genomics revisited
J Liu and B Rost
2002
Bioinformatics, 18, 922-933
(abstr, www, pdf)
|
Inferring sub-cellular localization through automated lexical analysis
R Nair and B Rost
2002
Bioinformatics, 18:Suppl 1, S78-S86
(abstr, www, pdf)
|
Comparing function and structure between entire proteomes
J Liu and B Rost
2001
Protein Science, 10, 1970-1979
(abstr, www, pdf)
|
Databases:
|
NLSdb: database of nuclear localization signals
R Nair, P Carter and B Rost
2003
Nucl Acid Res, 322, 397-399
(abstr, www, pdf)
|
LOC3D: annotate sub-cellular localization for protein structures
R Nair and B Rost
2003
Nucl Acids Res, 31, 3337-3340
(abstr, www, pdf)
|
CAFASP3 in the spotlight of EVA
VA Eyrich, IYY Koh, D Przybylski, O Grana, F Pazos, A Valencia and B Rost
2003
Proteins, 53 S6, 548-560
(abstr, www, pdf)
|
Better prediction of sub-cellular localization through evolution and structure
R Nair and B Rost
2003
Proteins, 53, 917-930
(abstr, www, pdf)
|
PEP: Predictions for Entire Proteomes
P Carter, J Liu and B Rost
2003
Nucl Acid Res, 31, 410-413
(abstr, www, pdf)
|
EVA: evaluation of protein structure prediction servers
IYY Koh, VA Eyrich, MA Mart’-Renom, D Przybylski, MS Madhusudhan, A Fiser, F Pazos, A Valencia, A Sali and B Rost
2003
Nucl Acids Res, 31, 3311-3315
(abstr, www, pdf)
|
Finding nuclear localization signals
M Cokol, R Nair and B Rost
2000
EMBO Reports, 1, 411-415
(abstr, www, pdf)
|
Twilight zone of protein sequence alignments
B Rost
1999
Protein Engineering, 12, 85-94
(abstr, www, pdf)
|
TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
B Rost
1995
Third International Conference on Intelligent Systems for Molecular Biology, , 314-321
(abstr, www, pdf)
|
Secondary structure:
|
DSSPcont: continuous secondary structure assignments for proteins
P Carter, CAF Andersen and B Rost
2003
Nucl Acids Res, 31, 3293-3295
(abstr, www, pdf)
|
The PredictProtein server
B Rost and J Liu
2003
Nucl Acids Res, 31, 3300-3304
(abstr, www, pdf)
|
NORSp: predictions of long regions without regular secondary structure
J Liu and B Rost
2003
Nucl Acids Res, 31, 3833-3835
(abstr, www, pdf)
|
Continuum secondary structure captures protein flexibility
CAF Andersen, AG Palmer, S Brunak and B Rost
2002
Structure, 10, 175-185
(abstr, www, pdf)
|
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
G Pollastri, D Przybylski, B Rost and P Baldi
2002
Proteins, 47, 228-235
(abstr, www, pdf)
|
Alignments grow, secondary structure prediction improves
D Przybylski and B Rost
2002
Proteins, 46, 197-205
(abstr, www, pdf)
|
Cafasp2: The second critical assessment of fully automated structure prediction methods
D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz and RLJ Dunbrack
2001
Proteins, 45 Suppl 5, S171-183
(abstr, www, pdf)
|
A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment
A Zemla, C Venclovas, K Fidelis and B Rost
1999
Proteins, 34, 220-223
(abstr, www, pdf)
|
Better 1D predictions by experts with machines. Proteins, Suppl
B Rost
1997
1, 192-197
(abstr, www, pdf)
|
PHD: predicting one-dimensional protein structure by profile based neural networks
B Rost and A Valencia
1996
Current Opinion in Biotechnology, 7, 457-461
(abstr, www, pdf)
|
Topology prediction for helical transmembrane proteins at 86% accuracy
B Rost, R Casadio and P Fariselli
1996
Protein Science, 5, 1704-1718
(abstr, www, pdf)
|
Progress of 1D protein structure prediction at last
B Rost and C Sander
1995
Proteins, 23, 295-300
(abstr, www, pdf)
|
1D secondary structure prediction through evolutionary profiles.
B Rost and C Sander
1994
in: 'Protein Structure by Distance Analysis' (eds H Bohr and S Brunak), , 257-276
(abstr, www, pdf)
|
Redefining the goals of protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
Journal of Molecular Biology, 235, 13-26
(abstr, www, pdf)
|
Evolution and neural networks - protein secondary structure prediction above 71% accuracy
B Rost, C Sander and R Schneider
1994
27th Hawaii International Conference on System Sciences, 5, 385-394
(abstr, www, pdf)
|
Combining evolutionary information and neural networks to predict protein secondary structure
B Rost and C Sander
1994
Proteins, 19, 55-72
(abstr, www, pdf)
|
PHD - an automatic server for protein secondary structure prediction
B Rost, C Sander and R Schneider
1994
CABIOS, 10, 53-60
(abstr, www, pdf)
|
Secondary structure prediction of all-helical proteins in two states
B Rost and C Sander
1993
Protein Engineering, 6, 831-836
(abstr, www, pdf)
|
Prediction of protein secondary structure at better than 70% accuracy
B Rost and C Sander
1993
Journal of Molecular Biology, 232, 584-599
(abstr, www, pdf)
|
Improved prediction of protein secondary structure by use of sequence profiles and neural networks
B Rost and C Sander
1993
Proceedings of the National Academy of Sciences, 90, 7558-7562
(abstr, www, pdf)
|
Jury returns on structure prediction
B Rost and C Sander
1992
Nature, 360, 540
(abstr, www, pdf)
|
Exercising multi-layered networks on protein secondary structure
B Rost and C Sander
1992
Neural Networks: From Biology to High Energy Physics, 3, 209-220
(abstr, www, pdf)
|
Suc-cellular localization:
|
Mimicking cellular sorting improves prediction of Subcellular Localization.
R Nair and B Rost
2005
Journal of Molecular Biology 2005 Apr 22;348(1):85-100.
(abstr, www, pdf)
|
NMPdb: Database of Nuclear Matrix Proteins.
S Mika and B Rost
2005
Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D160-3.
(abstr, www, pdf)
|
Protein function:
|
Mimicking cellular sorting improves prediction of Subcellular Localization.
R Nair and B Rost
2005
Journal of Molecular Biology 2005 Apr 22;348(1):85-100.
(abstr, www, pdf)
|
CASP6 assessment of contact prediction
O. Grana, D. Baker, R.M. MacCallum, J. Meiler, M. Punta, B. Rost, M. L. Tress, and A. Valencia
2005
Proteins 2005 61 Suppl 7:214-24
(abstr, | |
