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Proteins
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2021
Dallago C
,
Schütze K
,
Heinzinger M
,
Olenyi T
,
Littmann M
,
Lu AX
,
Yang KK
,
Min S
,
Yoon S
,
Morton JT
, et al.
Learned Embeddings from Deep Learning to Visualize and Predict Protein Sets.
Curr Protoc. 2021 ;1(5):e113.
Bernhofer M
,
Dallago C
,
Karl T
,
Satagopam V
,
Heinzinger M
,
Littmann M
,
Olenyi T
,
Qiu J
,
Schütze K
,
Yachdav G
, et al.
PredictProtein - Predicting Protein Structure and Function for 29 Years.
Nucleic Acids Res. 2021 ;49(W1):W535-W540.
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.
Qiu J
,
Nechaev D
,
Rost B
.
Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human.
BMC Bioinformatics. 2020 ;21(1):452.
Reeb J
,
Wirth T
,
Rost B
.
Variant effect predictions capture some aspects of deep mutational scanning experiments.
BMC Bioinformatics. 2020 ;21(1):107.
2015
O'Donoghue SI
,
Sabir KS
,
Kalemanov M
,
Stolte C
,
Wellmann B
,
Ho V
,
Roos M
,
Perdigão N
,
Buske FA
,
Heinrich J
, et al.
Aquaria: simplifying discovery and insight from protein structures.
Nat Methods. 2015 ;12(2):98-9.
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.
Goldberg T
,
Hecht M
,
Hamp T
,
Karl T
,
Yachdav G
,
Ahmed N
,
Altermann U
,
Angerer P
,
Ansorge S
,
Balasz K
, et al.
LocTree3 prediction of localization.
Nucleic Acids Res. 2014 ;42(Web Server issue):W350-5.
Yachdav G
,
Kloppmann E
,
Kaján L
,
Hecht M
,
Goldberg T
,
Hamp T
,
Hönigschmid P
,
Schafferhans A
,
Roos M
,
Bernhofer M
, et al.
PredictProtein--an open resource for online prediction of protein structural and functional features.
Nucleic Acids Res. 2014 ;42(Web Server issue):W337-43.
2013
Hamp T
,
Kassner R
,
Seemayer S
,
Vicedo E
,
Schaefer C
,
Achten D
,
Auer F
,
Boehm A
,
Braun T
,
Hecht M
, et al.
Homology-based inference sets the bar high for protein function prediction.
BMC Bioinformatics. 2013 ;14 Suppl 3:S7.
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
Hamp T
,
Rost B
.
Alternative protein-protein interfaces are frequent exceptions.
PLoS Comput Biol. 2012 ;8(8):e1002623.
Schaefer C
,
Bromberg Y
,
Achten D
,
Rost B
.
Disease-related mutations predicted to impact protein function.
BMC Genomics. 2012 ;13 Suppl 4:S11.
Goldberg T
,
Hamp T
,
Rost B
.
LocTree2 predicts localization for all domains of life.
Bioinformatics. 2012 ;28(18):i458-i465.
Schaefer C
,
Rost B
.
Predict impact of single amino acid change upon protein structure.
BMC Genomics. 2012 ;13 Suppl 4:S4.
Schaefer C
,
Meier A
,
Rost B
,
Bromberg Y
.
SNPdbe: constructing an nsSNP functional impacts database.
Bioinformatics. 2012 ;28(4):601-2.
2011
Rastogi S
,
Rost B
.
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana.
Nucleic Acids Res. 2011 ;39(Database issue):D230-4.
Schlessinger A
,
Schaefer C
,
Vicedo E
,
Schmidberger M
,
Punta M
,
Rost B
.
Protein disorder--a breakthrough invention of evolution?
. Curr Opin Struct Biol. 2011 ;21(3):412-8.
2010
Rastogi S
,
Rost B
.
Bioinformatics predictions of localization and targeting.
Methods Mol Biol. 2010 ;619:285-305.
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.
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.
Bertonati C
,
Punta M
,
Fischer M
,
Yachdav G
,
Forouhar F
,
Zhou W
,
Kuzin AP
,
Seetharaman J
,
Abashidze M
,
Ramelot TA
, et al.
Structural genomics reveals EVE as a new ASCH/PUA-related domain.
Proteins. 2009 ;75(3):760-73.
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
Bromberg Y
,
Rost B
.
Comprehensive in silico mutagenesis highlights functionally important residues in proteins.
Bioinformatics. 2008 ;24(16):i207-12.
Punta M
,
Rost B
.
Neural networks predict protein structure and function.
Methods Mol Biol. 2008 ;458:203-30.
Przybylski D
,
Rost B
.
Powerful fusion: PSI-BLAST and consensus sequences.
Bioinformatics. 2008 ;24(18):1987-93.
Trott O
,
Siggers K
,
Rost B
,
Palmer AG
.
Protein conformational flexibility prediction using machine learning.
J Magn Reson. 2008 ;192(1):37-47.
Nair R
,
Rost B
.
Protein subcellular localization prediction using artificial intelligence technology.
Methods Mol Biol. 2008 ;484:435-63.
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.
Ofran Y
,
Rost B
.
ISIS: interaction sites identified from sequence.
Bioinformatics. 2007 ;23(2):e13-6.
Schlessinger A
,
Punta M
,
Rost B
.
Natively unstructured regions in proteins identified from contact predictions.
Bioinformatics. 2007 ;23(18):2376-84.
Liu J
,
Montelione GT
,
Rost B
.
Novel leverage of structural genomics.
Nat Biotechnol. 2007 ;25(8):849-51.
Ofran Y
,
Rost B
.
Protein-protein interaction hotspots carved into sequences.
PLoS Comput Biol. 2007 ;3(7):e119.
Bromberg Y
,
Rost B
.
SNAP: predict effect of non-synonymous polymorphisms on function.
Nucleic Acids Res. 2007 ;35(11):3823-35.
2006
Ofran Y
,
Yachdav G
,
Mozes E
,
Soong T-T
,
Nair R
,
Rost B
.
Create and assess protein networks through molecular characteristics of individual proteins.
Bioinformatics. 2006 ;22(14):e402-7.
Liu J
,
Gough J
,
Rost B
.
Distinguishing protein-coding from non-coding RNAs through support vector machines.
PLoS Genet. 2006 ;2(4):e29.
Schlessinger A
,
Ofran Y
,
Yachdav G
,
Rost B
.
Epitome: database of structure-inferred antigenic epitopes.
Nucleic Acids Res. 2006 ;34(Database issue):D777-80.
Berman HM
,
Burley SK
,
Chiu W
,
Sali A
,
Adzhubei A
,
Bourne PE
,
Bryant SH
,
Dunbrack RL
,
Fidelis K
,
Frank J
, et al.
Outcome of a workshop on archiving structural models of biological macromolecules.
Structure. 2006 ;14(8):1211-7.
Schlessinger A
,
Yachdav G
,
Rost B
.
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics. 2006 ;22(7):891-3.
Mika S
,
Rost B
.
Protein-protein interactions more conserved within species than across species.
PLoS Comput Biol. 2006 ;2(7):e79.
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.
Snyder DA
,
Chen Y
,
Denissova NG
,
Acton T
,
Aramini JM
,
Ciano M
,
Karlin R
,
Liu J
,
Manor P
,
Rajan PA
, et al.
Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination.
J Am Chem Soc. 2005 ;127(47):16505-11.
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