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Computational Biology
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2021
O'Donoghue SI
,
Schafferhans A
,
Sikta N
,
Stolte C
,
Kaur S
,
Ho BK
,
Anderson S
,
Procter JB
,
Dallago C
,
Bordin N
, et al.
SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms.
Mol Syst Biol. 2021 ;17(9):e10079.
2020
Qiu J
,
Bernhofer M
,
Heinzinger M
,
Kemper S
,
Norambuena T
,
Melo F
,
Rost B
.
ProNA2020 predicts protein-DNA, protein-RNA, and protein-protein binding proteins and residues from sequence.
J Mol Biol. 2020 ;432(7):2428-2443.
Reeb J
,
Wirth T
,
Rost B
.
Variant effect predictions capture some aspects of deep mutational scanning experiments.
BMC Bioinformatics. 2020 ;21(1):107.
2014
Feiglin A
,
Ashkenazi S
,
Schlessinger A
,
Rost B
,
Ofran Y
.
Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence.
Mol Biosyst. 2014 ;10(4):787-94.
Kaján L
,
Hopf TA
,
Kalaš M
,
Marks DS
,
Rost B
.
FreeContact: fast and free software for protein contact prediction from residue co-evolution.
BMC Bioinformatics. 2014 ;15:85.
Rost B
.
ISCB: past-present perspective for the International Society for Computational Biology.
Bioinformatics. 2014 ;30(1):143-5.
2013
Rost B
.
ISCB: past-present perspective for the International Society for Computational Biology.
Bioinformatics. 2013 ;29(24):3243-5.
Radivojac P
,
Clark WT
,
Oron TRonnen
,
Schnoes AM
,
Wittkop T
,
Sokolov A
,
Graim K
,
Funk C
,
Verspoor K
,
Ben-Hur A
, et al.
A large-scale evaluation of computational protein function prediction.
Nat Methods. 2013 ;10(3):221-7.
2012
Schaefer C
,
Bromberg Y
,
Achten D
,
Rost B
.
Disease-related mutations predicted to impact protein function.
BMC Genomics. 2012 ;13 Suppl 4:S11.
Rost B
,
Gaasterland T
,
Lengauer T
,
Linial M
,
Markel S
,
McKay BJMorrison
,
Schneider R
,
Horton P
,
Kelso J
.
Paving the future: finding suitable ISMB venues.
Bioinformatics. 2012 ;28(19):2556-9.
Schaefer C
,
Rost B
.
Predict impact of single amino acid change upon protein structure.
BMC Genomics. 2012 ;13 Suppl 4:S4.
Kloppmann E
,
Punta M
,
Rost B
.
Structural genomics plucks high-hanging membrane proteins.
Curr Opin Struct Biol. 2012 ;22(3):326-32.
2011
Shi W
,
Punta M
,
Bohon J
,
J Sauder M
,
D'Mello R
,
Sullivan M
,
Toomey J
,
Abel D
,
Lippi M
,
Passerini A
, et al.
Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy.
Genome Res. 2011 ;21(6):898-907.
Schönbach C
,
Tan TWee
,
Kelso J
,
Rost B
,
Nathan S
,
Ranganathan S
.
InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia.
BMC Genomics. 2011 ;12 Suppl 3:S1.
Ranganathan S
,
Schönbach C
,
Kelso J
,
Rost B
,
Nathan S
,
Tan TWee
.
Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.
BMC Bioinformatics. 2011 ;12 Suppl 13:S1.
2010
Rastogi S
,
Rost B
.
Bioinformatics predictions of localization and targeting.
Methods Mol Biol. 2010 ;619:285-305.
Love J
,
Mancia F
,
Shapiro L
,
Punta M
,
Rost B
,
Girvin M
,
Wang D-N
,
Zhou M
,
Hunt JF
,
Szyperski T
, et al.
The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins.
J Struct Funct Genomics. 2010 ;11(3):191-9.
Schaefer C
,
Schlessinger A
,
Rost B
.
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be.
Bioinformatics. 2010 ;26(5):625-31.
2009
Bromberg Y
,
Rost B
.
Correlating protein function and stability through the analysis of single amino acid substitutions.
BMC Bioinformatics. 2009 ;10 Suppl 8:S8.
Moult J
,
Fidelis K
,
Kryshtafovych A
,
Rost B
,
Tramontano A
.
Critical assessment of methods of protein structure prediction - Round VIII.
Proteins. 2009 ;77 Suppl 9:1-4.
Cozzetto D
,
Kryshtafovych A
,
Fidelis K
,
Moult J
,
Rost B
,
Tramontano A
.
Evaluation of template-based models in CASP8 with standard measures.
Proteins. 2009 ;77 Suppl 9:18-28.
Schlessinger A
,
Punta M
,
Yachdav G
,
Kaján L
,
Rost B
.
Improved disorder prediction by combination of orthogonal approaches.
PLoS One. 2009 ;4(2):e4433.
Galea CA
,
High AA
,
Obenauer JC
,
Mishra A
,
Park C-G
,
Punta M
,
Schlessinger A
,
Ma J
,
Rost B
,
Slaughter CA
, et al.
Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome.
J Proteome Res. 2009 ;8(1):211-26.
Bigelow H
,
Rost B
.
Online tools for predicting integral membrane proteins.
Methods Mol Biol. 2009 ;528:3-23.
Dessailly BH
,
Nair R
,
Jaroszewski L
,
J Fajardo E
,
Kouranov A
,
Lee D
,
Fiser A
,
Godzik A
,
Rost B
,
Orengo C
.
PSI-2: structural genomics to cover protein domain family space.
Structure. 2009 ;17(6):869-81.
Nair R
,
Liu J
,
Soong T-T
,
Acton TB
,
Everett JK
,
Kouranov A
,
Fiser A
,
Godzik A
,
Jaroszewski L
,
Orengo C
, et al.
Structural genomics is the largest contributor of novel structural leverage.
J Struct Funct Genomics. 2009 ;10(2):181-91.
W Price N
,
Chen Y
,
Handelman SK
,
Neely H
,
Manor P
,
Karlin R
,
Nair R
,
Liu J
,
Baran M
,
Everett J
, et al.
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.
Nat Biotechnol. 2009 ;27(1):51-7.
Kernytsky A
,
Rost B
.
Using genetic algorithms to select most predictive protein features.
Proteins. 2009 ;75(1):75-88.
2008
Lippi M
,
Passerini A
,
Punta M
,
Rost B
,
Frasconi P
.
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Bioinformatics. 2008 ;24(18):2094-5.
Soong T-T
,
Wrzeszczynski KO
,
Rost B
.
Physical protein-protein interactions predicted from microarrays.
Bioinformatics. 2008 ;24(22):2608-14.
Bromberg Y
,
Yachdav G
,
Rost B
.
SNAP predicts effect of mutations on protein function.
Bioinformatics. 2008 ;24(20):2397-8.
2007
Moult J
,
Fidelis K
,
Kryshtafovych A
,
Rost B
,
Hubbard T
,
Tramontano A
.
Critical assessment of methods of protein structure prediction-Round VII.
Proteins. 2007 ;69 Suppl 8:3-9.
Schlessinger A
,
Liu J
,
Rost B
.
Natively unstructured loops differ from other loops.
PLoS Comput Biol. 2007 ;3(7):e140.
Bromberg Y
,
Rost B
.
SNAP: predict effect of non-synonymous polymorphisms on function.
Nucleic Acids Res. 2007 ;35(11):3823-35.
2006
Passerini A
,
Punta M
,
Ceroni A
,
Rost B
,
Frasconi P
.
Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.
Proteins. 2006 ;65(2):305-16.
Schlessinger A
,
Yachdav G
,
Rost B
.
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics. 2006 ;22(7):891-3.
2005
Ofran Y
,
Punta M
,
Schneider R
,
Rost B
.
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
Drug Discov Today. 2005 ;10(21):1475-82.
Graña O
,
Baker D
,
MacCallum RM
,
Meiler J
,
Punta M
,
Rost B
,
Tress ML
,
Valencia A
.
CASP6 assessment of contact prediction.
Proteins. 2005 ;61 Suppl 7:214-24.
Moult J
,
Fidelis K
,
Rost B
,
Hubbard T
,
Tramontano A
.
Critical assessment of methods of protein structure prediction (CASP)--round 6.
Proteins. 2005 ;61 Suppl 7:3-7.
2004
Wrzeszczynski KO
,
Rost B
.
Cataloging proteins in cell cycle control.
Methods Mol Biol. 2004 ;241:219-33.
Liu J
,
Rost B
.
Sequence-based prediction of protein domains.
Nucleic Acids Res. 2004 ;32(12):3522-30.
2003
Nair R
,
Rost B
.
Better prediction of sub-cellular localization by combining evolutionary and structural information.
Proteins. 2003 ;53(4):917-30.
Eyrich VA
,
Przybylski D
,
Y Y Koh I
,
Graña O
,
Pazos F
,
Valencia A
,
Rost B
.
CAFASP3 in the spotlight of EVA.
Proteins. 2003 ;53 Suppl 6:548-60.
Ofran Y
,
Rost B
.
Predicted protein-protein interaction sites from local sequence information.
FEBS Lett. 2003 ;544(1-3):236-9.
Rost B
.
Prediction in 1D: secondary structure, membrane helices, and accessibility.
Methods Biochem Anal. 2003 ;44:559-87.
Andersen CAF
,
Rost B
.
Secondary structure assignment.
Methods Biochem Anal. 2003 ;44:341-63.
2002
Rost B
,
Honig B
,
Valencia A
.
Bioinformatics in structural genomics.
Bioinformatics. 2002 ;18(7):897-8.
Chen CPeter
,
Rost B
.
Long membrane helices and short loops predicted less accurately.
Protein Sci. 2002 ;11(12):2766-73.
Liu J
,
Tan H
,
Rost B
.
Loopy proteins appear conserved in evolution.
J Mol Biol. 2002 ;322(1):53-64.
Nair R
,
Rost B
.
Sequence conserved for subcellular localization.
Protein Sci. 2002 ;11(12):2836-47.
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