Publications

Found 38 results

Filters: Keyword is Sequence Analysis, Protein [Clear All Filters]

2021

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.

2014

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.

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.

2012

Goldberg T, Hamp T, Rost B. LocTree2 predicts localization for all domains of life. Bioinformatics. 2012 ;28(18):i458-i465.

2009

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.

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.

2008

Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics. 2008 ;24(16):i207-12.

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.

Przybylski D, Rost B. Powerful fusion: PSI-BLAST and consensus sequences. Bioinformatics. 2008 ;24(18):1987-93.

2007

Przybylski D, Rost B. Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res. 2007 ;35(7):2238-46.

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.

Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence. Bioinformatics. 2007 ;23(13):i347-53.

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.

Bigelow H, Rost B. PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res. 2006 ;34(Web Server issue):W186-8.

2005

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.

Punta M, Rost B. PROFcon: novel prediction of long-range contacts. Bioinformatics. 2005 ;21(13):2960-8.

2004

Liu J, Rost B. CHOP: parsing proteins into structural domains. Nucleic Acids Res. 2004 ;32(Web Server issue):W569-71.

Liu J, Rost B. CHOP proteins into structural domain-like fragments. Proteins. 2004 ;55(3):678-88.

Przybylski D, Rost B. Improving fold recognition without folds. J Mol Biol. 2004 ;341(1):255-69.

Nair R, Rost B. LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res. 2004 ;32(Web Server issue):W517-21.

Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B. Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res. 2004 ;32(8):2566-77.

Rost B, Yachdav G, Liu J. The PredictProtein server. Nucleic Acids Res. 2004 ;32(Web Server issue):W321-6.

Liu J, Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res. 2004 ;32(12):3522-30.

2003

Y Y Koh I, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, et al. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003 ;31(13):3311-5.

Nair R, Rost B. LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res. 2003 ;31(13):3337-40.

Eyrich VA, Rost B. META-PP: single interface to crucial prediction servers. Nucleic Acids Res. 2003 ;31(13):3308-10.

Liu J, Rost B. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res. 2003 ;31(13):3833-5.

Rost B, Liu J. The PredictProtein server. Nucleic Acids Res. 2003 ;31(13):3300-4.

Kernytsky A, Rost B. Static benchmarking of membrane helix predictions. Nucleic Acids Res. 2003 ;31(13):3642-4.

Mika S, Rost B. UniqueProt: Creating representative protein sequence sets. Nucleic Acids Res. 2003 ;31(13):3789-91.

2002

Nair R, Rost B. Inferring sub-cellular localization through automated lexical analysis. Bioinformatics. 2002 ;18 Suppl 1:S78-86.

Liu J, Rost B. Target space for structural genomics revisited. Bioinformatics. 2002 ;18(7):922-33.