Publications

Found 86 results
Filters: Keyword is Proteins  [Clear All Filters]
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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