Publications

Found 36 results
Filters: Keyword is Software and Author is Rost, Burkhard  [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.
Reeb J, Wirth T, Rost B. Variant effect predictions capture some aspects of deep mutational scanning experiments. BMC Bioinformatics. 2020 ;21(1):107.
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.
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.
Cejuela JMiguel, McQuilton P, Ponting L, Marygold SJ, Stefancsik R, Millburn GH, Rost B. tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database (Oxford). 2014 ;2014:bau033.
2013
Rost B. ISCB: past-present perspective for the International Society for Computational Biology. Bioinformatics. 2013 ;29(24):3243-5.
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
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N. MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res. 2010 ;38(Web Server issue):W523-8.
2009
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.
Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Curr Opin Drug Discov Devel. 2009 ;12(3):408-19.
Bigelow H, Rost B. Online tools for predicting integral membrane proteins. Methods Mol Biol. 2009 ;528:3-23.
2008
Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics. 2008 ;24(20):2397-8.
2007
Przybylski D, Rost B. Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. Nucleic Acids Res. 2007 ;35(7):2238-46.
2006
Schlessinger A, Yachdav G, Rost B. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics. 2006 ;22(7):891-3.
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
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.
Graña O, Eyrich VA, Pazos F, Rost B, Valencia A. EVAcon: a protein contact prediction evaluation service. Nucleic Acids Res. 2005 ;33(Web Server issue):W347-51.
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.
Nair R, Rost B. LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res. 2004 ;32(Web Server issue):W517-21.
Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res. 2004 ;32(Web Server issue):W634-7.
Rost B, Yachdav G, Liu J. The PredictProtein server. Nucleic Acids Res. 2004 ;32(Web Server issue):W321-6.
Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, et al. The protein target list of the Northeast Structural Genomics Consortium. Proteins. 2004 ;56(2):181-7.
2003
Carter P, Andersen CAF, Rost B. DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res. 2003 ;31(13):3293-5.
Liu J, Rost B. NORSp: Predictions of long regions without regular secondary structure. Nucleic Acids Res. 2003 ;31(13):3833-5.
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.
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
Andersen CAF, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure. 2002 ;10(2):175-84.
Chen CPeter, Rost B. State-of-the-art in membrane protein prediction. Appl Bioinformatics. 2002 ;1(1):21-35.
Chen CPeter, Kernytsky A, Rost B. Transmembrane helix predictions revisited. Protein Sci. 2002 ;11(12):2774-91.