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Burkhard Rost
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Research Profile (preview)
Concepts & Ideas
Chemicals & Drugs
Procedures
Occupations
Activities & Behaviors
Genes & Molecular Sequences
Physiology
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Network (preview)
19
Liu, Jinfeng
14
Nair, Rajesh
11
Ofran, Yanay
10
Punta, Marco
9
Przybylski, Dariusz
8
Yachdav, Guy
7
Montelione, Gaetano
6
Schlessinger, Avner
6
Acton, Thomas
6
Eyrich, Volker
5
Mika, Sven
5
Galvez, Carmen
5
Wrzeszczynski, Kazimierz
4
Xiao, Rong
4
Pazos, Florencio
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All Publications
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2009: Eletsky Alexander; Sukumaran Dinesh K; Xiao Rong; Acton Thomas B; Rost Burkhard; Montelione Gaetano T; Szyperski Thomas
NMR structure of protein YvyC from Bacillus subtilis reveals unexpected structural similarity between two PFAM families.
Proteins 2009;76(4):1037-41.
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2009: Bromberg Yana; Overton John; Vaisse Christian; Leibel Rudolph L; Rost Burkhard
In silico mutagenesis: a case study of the melanocortin 4 receptor.
The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009;23(9):3059-69.
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2009: Dessailly Benoît H; Nair Rajesh; Jaroszewski Lukasz; Fajardo J Eduardo; Kouranov Andrei; Lee David; Fiser Andras; Godzik Adam; Rost Burkhard; Orengo Christine
PSI-2: structural genomics to cover protein domain family space.
Structure (London, England : 1993) 2009;17(6):869-81.
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2009: Bromberg Yana; Yachdav Guy; Ofran Yanay; Schneider Reinhard; Rost Burkhard
New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.
Current opinion in drug discovery & development 2009;12(3):408-19.
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2009: Bertonati Claudia; Punta Marco; Fischer Markus; Yachdav Guy; Forouhar Farhad; Zhou Weihong; Kuzin Alexander P; Seetharaman Jayaraman; Abashidze Mariam; Ramelot Theresa A; Kennedy Michael A; Cort John R; Belachew Adam; Hunt John F; Tong Liang; Montelione Gaetano T; Rost Burkhard
Structural genomics reveals EVE as a new ASCH/PUA-related domain.
Proteins 2009;75(3):760-73.
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2009: Nair Rajesh; Liu Jinfeng; Soong Ta-Tsen; Acton Thomas B; Everett John K; Kouranov Andrei; Fiser Andras; Godzik Adam; Jaroszewski Lukasz; Orengo Christine; Montelione Gaetano T; Rost Burkhard
Structural genomics is the largest contributor of novel structural leverage.
Journal of structural and functional genomics 2009;10(2):181-91.
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2009: Liu Gaohua; Forouhar Farhad; Eletsky Alexander; Atreya Hanudatta S; Aramini James M; Xiao Rong; Huang Yuanpeng J; Abashidze Mariam; Seetharaman Jayaraman; Liu Jinfeng; Rost Burkhard; Acton Thomas; Montelione Gaetano T; Hunt John F; Szyperski Thomas
NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway.
Journal of structural and functional genomics 2009;10(2):127-36.
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2009: Kernytsky Andrew; Rost Burkhard
Using genetic algorithms to select most predictive protein features.
Proteins 2009;75(1):75-88.
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2009: Wrzeszczynski Kazimierz O; Rost Burkhard
Cell cycle kinases predicted from conserved biophysical properties.
Proteins 2009;74(3):655-68.
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2009: Price W Nicholson; Chen Yang; Handelman Samuel K; Neely Helen; Manor Philip; Karlin Richard; Nair Rajesh; Liu Jinfeng; Baran Michael; Everett John; Tong Saichiu N; Forouhar Farhad; Swaminathan Swarup S; Acton Thomas; Xiao Rong; Luft Joseph R; Lauricella Angela; DeTitta George T; Rost Burkhard; Montelione Gaetano T; Hunt John F
Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.
Nature biotechnology 2009;27(1):51-7.
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2009: Bromberg Yana; Rost Burkhard
Correlating protein function and stability through the analysis of single amino acid substitutions.
BMC bioinformatics 2009;10 Suppl 8():S8.
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2009: Schlessinger Avner; Punta Marco; Yachdav Guy; Kajan Laszlo; Rost Burkhard
Improved disorder prediction by combination of orthogonal approaches.
PloS one 2009;4(2):e4433.
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2009: Bigelow Henry; Rost Burkhard
Online tools for predicting integral membrane proteins.
Methods in molecular biology (Clifton, N.J.) 2009;528():3-23.
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2008: Ofran Yanay; Schlessinger Avner; Rost Burkhard
Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes.
Journal of immunology (Baltimore, Md. : 1950) 2008;181(9):6230-5.
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2008: Soong Ta-Tsen; Wrzeszczynski Kazimierz O; Rost Burkhard
Physical protein-protein interactions predicted from microarrays.
Bioinformatics (Oxford, England) 2008;24(22):2608-14.
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2008: Bromberg Yana; Yachdav Guy; Rost Burkhard
SNAP predicts effect of mutations on protein function.
Bioinformatics (Oxford, England) 2008;24(20):2397-8.
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2008: Przybylski Dariusz; Rost Burkhard
Powerful fusion: PSI-BLAST and consensus sequences.
Bioinformatics (Oxford, England) 2008;24(18):1987-93.
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2008: Lippi Marco; Passerini Andrea; Punta Marco; Rost Burkhard; Frasconi Paolo
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Bioinformatics (Oxford, England) 2008;24(18):2094-5.
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2008: Bromberg Yana; Rost Burkhard
Comprehensive in silico mutagenesis highlights functionally important residues in proteins.
Bioinformatics (Oxford, England) 2008;24(16):i207-12.
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2008: Trott Oleg; Siggers Keri; Rost Burkhard; Palmer Arthur G
Protein conformational flexibility prediction using machine learning.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2008;192(1):37-47.
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2008: Punta Marco; Rost Burkhard
Neural networks predict protein structure and function.
Methods in molecular biology (Clifton, N.J.) 2008;458():203-30.
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2008: Nair Rajesh; Rost Burkhard
Protein subcellular localization prediction using artificial intelligence technology.
Methods in molecular biology (Clifton, N.J.) 2008;484():435-63.
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2007: Schlessinger Avner; Punta Marco; Rost Burkhard
Natively unstructured regions in proteins identified from contact predictions.
Bioinformatics (Oxford, England) 2007;23(18):2376-84.
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2007: Schlessinger Avner; Liu Jinfeng; Rost Burkhard
Natively unstructured loops differ from other loops.
PLoS computational biology 2007;3(7):e140.
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2007: Ofran Yanay; Mysore Venkatesh; Rost Burkhard
Prediction of DNA-binding residues from sequence.
Bioinformatics (Oxford, England) 2007;23(13):i347-53.
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2007: Ofran Yanay; Rost Burkhard
Protein-protein interaction hotspots carved into sequences.
PLoS computational biology 2007;3(7):e119.
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2007: Punta Marco; Forrest Lucy R; Bigelow Henry; Kernytsky Andrew; Liu Jinfeng; Rost Burkhard
Membrane protein prediction methods.
Methods (San Diego, Calif.) 2007;41(4):460-74.
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2007: Ofran Yanay; Rost Burkhard
ISIS: interaction sites identified from sequence.
Bioinformatics (Oxford, England) 2007;23(2):e13-6.
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2007: Bromberg Yana; Rost Burkhard
SNAP: predict effect of non-synonymous polymorphisms on function.
Nucleic acids research 2007;35(11):3823-35.
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2007: Przybylski Dariusz; Rost Burkhard
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.
Nucleic acids research 2007;35(7):2238-46.
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2006: Passerini Andrea; Punta Marco; Ceroni Alessio; Rost Burkhard; Frasconi Paolo
Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.
Proteins 2006;65(2):305-16.
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2006: Ofran Yanay; Yachdav Guy; Mozes Eyal; Soong Ta-tsen; Nair Rajesh; Rost Burkhard
Create and assess protein networks through molecular characteristics of individual proteins.
Bioinformatics (Oxford, England) 2006;22(14):e402-7.
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2006: Mika Sven; Rost Burkhard
Protein-protein interactions more conserved within species than across species.
PLoS computational biology 2006;2(7):e79.
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2006: Bigelow Henry; Rost Burkhard
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Nucleic acids research 2006;34(Web Server issue):W186-8.
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2006: Liu Jinfeng; Gough Julian; Rost Burkhard
Distinguishing protein-coding from non-coding RNAs through support vector machines.
PLoS genetics 2006;2(4):e29.
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2006: Schlessinger Avner; Yachdav Guy; Rost Burkhard
PROFbval: predict flexible and rigid residues in proteins.
Bioinformatics (Oxford, England) 2006;22(7):891-3.
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2006: Schlessinger Avner; Ofran Yanay; Yachdav Guy; Rost Burkhard
Epitome: database of structure-inferred antigenic epitopes.
Nucleic acids research 2006;34(Database issue):D777-80.
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2005: Ofran Yanay; Punta Marco; Schneider Reinhard; Rost Burkhard
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
Drug discovery today 2005;10(21):1475-82.
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2005: Schlessinger Avner; Rost Burkhard
Protein flexibility and rigidity predicted from sequence.
Proteins 2005;61(1):115-26.
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2005: Graña Osvaldo; Eyrich Volker A; Pazos Florencio; Rost Burkhard; Valencia Alfonso
EVAcon: a protein contact prediction evaluation service.
Nucleic acids research 2005;33(Web Server issue):W347-51.
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2005: Punta Marco; Rost Burkhard
PROFcon: novel prediction of long-range contacts.
Bioinformatics (Oxford, England) 2005;21(13):2960-8.
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2005: Benach Jordi; Edstrom William C; Lee Insun; Das Kalyan; Cooper Bonnie; Xiao Rong; Liu Jinfeng; Rost Burkhard; Acton Thomas B; Montelione Gaetano T; Hunt John F
The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.
Acta crystallographica. Section D, Biological crystallography 2005;61(Pt 5):589-98.
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2005: Punta Marco; Rost Burkhard
Protein folding rates estimated from contact predictions.
Journal of molecular biology 2005;348(3):507-12.
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2005: Nair Rajesh; Rost Burkhard
Mimicking cellular sorting improves prediction of subcellular localization.
Journal of molecular biology 2005;348(1):85-100.
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2005: Mika Sven; Rost Burkhard
NMPdb: Database of Nuclear Matrix Proteins.
Nucleic acids research 2005;33(Database issue):D160-3.
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2005: Graña Osvaldo; Baker David; MacCallum Robert M; Meiler Jens; Punta Marco; Rost Burkhard; Tress Michael L; Valencia Alfonso
CASP6 assessment of contact prediction.
Proteins 2005;61 Suppl 7():214-24.
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2004: Mika Sven; Rost Burkhard
Protein names precisely peeled off free text.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i241-7.
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2004: Liu Jinfeng; Hegyi Hedi; Acton Thomas B; Montelione Gaetano T; Rost Burkhard
Automatic target selection for structural genomics on eukaryotes.
Proteins 2004;56(2):188-200.
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2004: Przybylski Dariusz; Rost Burkhard
Improving fold recognition without folds.
Journal of molecular biology 2004;341(1):255-69.
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2004: Mika Sven; Rost Burkhard
NLProt: extracting protein names and sequences from papers.
Nucleic acids research 2004;32(Web Server issue):W634-7.
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2004: Liu Jinfeng; Rost Burkhard
CHOP: parsing proteins into structural domains.
Nucleic acids research 2004;32(Web Server issue):W569-71.
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2004: Nair Rajesh; Rost Burkhard
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.
Nucleic acids research 2004;32(Web Server issue):W517-21.
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2004: Rost Burkhard; Yachdav Guy; Liu Jinfeng
The PredictProtein server.
Nucleic acids research 2004;32(Web Server issue):W321-6.
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2004: Wrzeszczynski K O; Rost B
Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes.
Cellular and molecular life sciences : CMLS 2004;61(11):1341-53.
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2004: Liu Jinfeng; Rost Burkhard
CHOP proteins into structural domain-like fragments.
Proteins 2004;55(3):678-88.
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2004: Liu Jinfeng; Rost Burkhard
Sequence-based prediction of protein domains.
Nucleic acids research 2004;32(12):3522-30.
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2004: Bigelow Henry R; Petrey Donald S; Liu Jinfeng; Przybylski Dariusz; Rost Burkhard
Predicting transmembrane beta-barrels in proteomes.
Nucleic acids research 2004;32(8):2566-77.
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2004: Wrzeszczynski Kazimierz O; Rost Burkhard
Cataloging proteins in cell cycle control.
Methods in molecular biology (Clifton, N.J.) 2004;241():219-33.
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2003: Rost B; Liu J; Nair R; Wrzeszczynski K O; Ofran Y
Automatic prediction of protein function.
Cellular and molecular life sciences : CMLS 2003;60(12):2637-50.
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2003: Nair Rajesh; Rost Burkhard
Better prediction of sub-cellular localization by combining evolutionary and structural information.
Proteins 2003;53(4):917-30.
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2003: Liu Jinfeng; Rost Burkhard
NORSp: Predictions of long regions without regular secondary structure.
Nucleic acids research 2003;31(13):3833-5.
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2003: Mika Sven; Rost Burkhard
UniqueProt: Creating representative protein sequence sets.
Nucleic acids research 2003;31(13):3789-91.
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2003: Kernytsky Andrew; Rost Burkhard
Static benchmarking of membrane helix predictions.
Nucleic acids research 2003;31(13):3642-4.
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2003: Nair Rajesh; Rost Burkhard
LOC3D: annotate sub-cellular localization for protein structures.
Nucleic acids research 2003;31(13):3337-40.
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2003: Koh Ingrid Y Y; Eyrich Volker A; Marti-Renom Marc A; Przybylski Dariusz; Madhusudhan Mallur S; Eswar Narayanan; Graña Osvaldo; Pazos Florencio; Valencia Alfonso; Sali Andrej; Rost Burkhard
EVA: Evaluation of protein structure prediction servers.
Nucleic acids research 2003;31(13):3311-5.
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2003: Eyrich Volker A; Rost Burkhard
META-PP: single interface to crucial prediction servers.
Nucleic acids research 2003;31(13):3308-10.
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2003: Rost Burkhard; Liu Jinfeng
The PredictProtein server.
Nucleic acids research 2003;31(13):3300-4.
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2003: Carter Phil; Andersen Claus A F; Rost Burkhard
DSSPcont: Continuous secondary structure assignments for proteins.
Nucleic acids research 2003;31(13):3293-5.
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2003: Ofran Yanay; Rost Burkhard
Predicted protein-protein interaction sites from local sequence information.
FEBS letters 2003;544(1-3):236-9.
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2003: Liu Jinfeng; Rost Burkhard
Domains, motifs and clusters in the protein universe.
Current opinion in chemical biology 2003;7(1):5-11.
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2003: Carter Phil; Liu Jinfeng; Rost Burkhard
PEP: Predictions for Entire Proteomes.
Nucleic acids research 2003;31(1):410-3.
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2003: Nair Rajesh; Carter Phil; Rost Burkhard
NLSdb: database of nuclear localization signals.
Nucleic acids research 2003;31(1):397-9.
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2003: Ofran Yanay; Rost Burkhard
Analysing six types of protein-protein interfaces.
Journal of molecular biology 2003;325(2):377-87.
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2003: Eyrich Volker A; Przybylski Dariusz; Koh Ingrid Y Y; Grana Osvaldo; Pazos Florencio; Valencia Alfonso; Rost Burkhard
CAFASP3 in the spotlight of EVA.
Proteins 2003;53 Suppl 6():548-60.
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2003: Rost Burkhard
Prediction in 1D: secondary structure, membrane helices, and accessibility.
Methods of biochemical analysis 2003;44():559-87.
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2003: Andersen Claus A F; Rost Burkhard
Secondary structure assignment.
Methods of biochemical analysis 2003;44():341-63.
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2002: Nair Rajesh; Rost Burkhard
Sequence conserved for subcellular localization.
Protein science : a publication of the Protein Society 2002;11(12):2836-47.
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2002: Chen Chien Peter; Kernytsky Andrew; Rost Burkhard
Transmembrane helix predictions revisited.
Protein science : a publication of the Protein Society 2002;11(12):2774-91.
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2002: Chen Chien Peter; Rost Burkhard
Long membrane helices and short loops predicted less accurately.
Protein science : a publication of the Protein Society 2002;11(12):2766-73.
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2002: Liu Jinfeng; Tan Hepan; Rost Burkhard
Loopy proteins appear conserved in evolution.
Journal of molecular biology 2002;322(1):53-64.
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2002: Liu Jinfeng; Rost Burkhard
Target space for structural genomics revisited.
Bioinformatics (Oxford, England) 2002;18(7):922-33.
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2002: Rost Burkhard
Did evolution leap to create the protein universe?
Current opinion in structural biology 2002;12(3):409-16.
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2002: Pollastri Gianluca; Przybylski Darisz; Rost Burkhard; Baldi Pierre
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles.
Proteins 2002;47(2):228-35.
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2002: Rost Burkhard
Enzyme function less conserved than anticipated.
Journal of molecular biology 2002;318(2):595-608.
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2002: Marti-Renom Marc A; Madhusudhan M S; Fiser András; Rost Burkhard; Sali Andrej
Reliability of assessment of protein structure prediction methods.
Structure (London, England : 1993) 2002;10(3):435-40.
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2002: Andersen Claus A F; Palmer Arthur G; Brunak Søren; Rost Burkhard
Continuum secondary structure captures protein flexibility.
Structure (London, England : 1993) 2002;10(2):175-84.
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2002: Przybylski Dariusz; Rost Burkhard
Alignments grow, secondary structure prediction improves.
Proteins 2002;46(2):197-205.
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2002: Chen Chien Peter; Rost Burkhard
State-of-the-art in membrane protein prediction.
Applied bioinformatics 2002;1(1):21-35.
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2002: Nair Rajesh; Rost Burkhard
Inferring sub-cellular localization through automated lexical analysis.
Bioinformatics (Oxford, England) 2002;18 Suppl 1():S78-86.
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2001: Eyrich V A; Martí-Renom M A; Przybylski D; Madhusudhan M S; Fiser A; Pazos F; Valencia A; Sali A; Rost B
EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinformatics (Oxford, England) 2001;17(12):1242-3.
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2001: Liu J; Rost B
Comparing function and structure between entire proteomes.
Protein science : a publication of the Protein Society 2001;10(10):1970-9.
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2001: Rost B; Eyrich V A
EVA: large-scale analysis of secondary structure prediction.
Proteins 2001;Suppl 5():192-9.
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2000: Cokol M; Nair R; Rost B
Finding nuclear localization signals.
EMBO reports 2000;1(5):411-5.
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2000: Rost B; Sander C
Third generation prediction of secondary structures.
Methods in molecular biology (Clifton, N.J.) 2000;143():71-95.
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