Research Topics
Species | B RostSummaryAffiliation: Columbia University Country: USA Publications
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Publications
Correlating protein function and stability through the analysis of single amino acid substitutionsYana Bromberg
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
BMC Bioinformatics 10:S8. 2009..However, experimental 3D structures are available for only 1% of all known proteins; the magnitude of stability change caused by a given mutation is more widely available...- The PredictProtein serverBurkhard Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 32:W321-6. 2004..For all services, users can submit their query either by electronic mail or interactively via the World Wide Web... - The PredictProtein serverBurkhard Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3300-4. 2003..Upon request, fold recognition by prediction-based threading is available. For all services, users can submit their query either by electronic mail or interactively from World Wide Web... - Automatic prediction of protein functionB Rost
Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, New York 10032, USA
Cell Mol Life Sci 60:2637-50. 2003..No matter how difficult the task, successes over the last few years have clearly paved the way for ab initio prediction of protein function... - Did evolution leap to create the protein universe?Burkhard Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, BB217, New York, NY 10032, USA
Curr Opin Struct Biol 12:409-16. 2002..Either way, after having harvested proteomes by applying standard tools, the challenge now seems to be to develop better methods for comparative proteomics... - Enzyme function less conserved than anticipatedBurkhard Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
J Mol Biol 318:595-608. 2002..In practice, the revised detailed estimates for the sequence conservation of enzyme function may provide important benchmarks for everyday sequence analysis and for more cautious automatic genome annotations... - EVA: large-scale analysis of secondary structure predictionB Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins . 2001..What is the limit of prediction accuracy? We shall see. All data are available through the EVA web site at [cubic.bioc.columbia.edu/eva/]. The raw data for the results presented are available at [eva]/sec/bup_common/2001_02_22/... - Alignments grow, secondary structure prediction improvesDariusz Przybylski
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
Proteins 46:197-205. 2002..iv) Improvement through family growth appears to saturate at some point. However, most families have not reached this saturation. Hence, we anticipate that prediction accuracy will continue to rise with database growth... - Loopy proteins appear conserved in evolutionJinfeng Liu
Department of Pharmacology, Columbia University, New York, NY 10032, USA
J Mol Biol 322:53-64. 2002..Overall, our analysis confirmed that proteins with non-regular structures appear to play important functional roles, and they may adopt as yet unknown types of protein structures... - Target space for structural genomics revisitedJinfeng Liu
Department of Pharmacology, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Bioinformatics 18:922-33. 2002..AVAILABILITY: All data are available from the authors, most results are summarized at: http://cubic.bioc.columbia.edu/genomes/RES/2002_bioinformatics/.. - Automatic target selection for structural genomics on eukaryotesJinfeng Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 56:188-200. 2004..Thus, our results suggested that it might be necessary to determine >40,000 structures to minimally cover the subset of five eukaryotic proteomes... - Structural genomics reveals EVE as a new ASCH/PUA-related domainClaudia Bertonati
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Proteins 75:760-73. 2009..Primary sequence information alone would have not been sufficient to reveal these evolutionary links... - Secondary structure assignmentClaus A F Andersen
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Methods Biochem Anal 44:341-63. 2003 - Neural networks predict protein structure and functionMarco Punta
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Methods Mol Biol 458:203-30. 2008..We discuss how to select an appropriate data set, how to choose and encode protein features into the neural network input, and how to assess the predictor's performance... - Protein-protein interactions more conserved within species than across speciesSven Mika
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
PLoS Comput Biol 2:e79. 2006..More comprehensive images of protein-protein networks will require the combination of many high-throughput methods, including in silico inferences and predictions. http://www.rostlab.org/results/2006/ppi_homology/.. - PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteinsHenry Bigelow
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Nucleic Acids Res 34:W186-8. 2006..The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at http://rostlab.org/services/proftmb... - CHOP: parsing proteins into structural domainsJinfeng Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 32:W569-71. 2004..CHOP results are precompiled for many entirely sequenced proteomes. The service is available at http://www.rostlab.org/services/CHOP/... - Online tools for predicting integral membrane proteinsHenry Bigelow
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Methods Mol Biol 528:3-23. 2009..Because of this, the best approach is an opportunistic one: submit the protein of interest to all methods and choose the results with the highest confidence scores... - State-of-the-art in membrane protein predictionChien Peter Chen
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Appl Bioinformatics 1:21-35. 2002..However, the computational biologists will have to improve their methods considerably before they reach the levels of accuracy they claim... - Structural genomics is the largest contributor of novel structural leverageRajesh Nair
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
J Struct Funct Genomics 10:181-91. 2009..If the success of the PSI continues, it may just take another approximately15 years to cover most sequences in the current UniProt database... - Inferring sub-cellular localization through automated lexical analysisRajesh Nair
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Bioinformatics 18:S78-86. 2002..LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes... - Using genetic algorithms to select most predictive protein featuresAndrew Kernytsky
Department of Biochemistry and Molecular Biophysics, Columbia University, New York 10032, New York, USA
Proteins 75:75-88. 2009..The final framework manages to effectively sample a feature space that is far too large for exhaustive enumeration. We demonstrate the power of the concept by applying it to prediction of protein enzymatic activity... - Protein flexibility and rigidity predicted from sequenceAvner Schlessinger
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 61:115-26. 2005..Our method had not been set up to address any of the tasks in those 4 case studies. Therefore, we expect that this method will assist in many attempts at inferring aspects of function... - PROFbval: predict flexible and rigid residues in proteinsAvner Schlessinger
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Bioinformatics 22:891-3. 2006..AVAILABILITY: http://www.rostlab.org/services/profbval CONTACT: profbval@rostlab.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online... - Continuum secondary structure captures protein flexibilityClaus A F Andersen
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Structure 10:175-84. 2002..Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction... - Comparing function and structure between entire proteomesJ Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Protein Sci 10:1970-9. 2001..These numbers may or may not suggest that there are 1200-2600 folds in the universe of protein structures. All predictions are available at http://cubic.bioc.columbia.edu/genomes... - EVA: continuous automatic evaluation of protein structure prediction serversV A Eyrich
Department of Chemistry, Columbia University, 3000 Broadway MC 3136, New York, NY 10027, USA
Bioinformatics 17:1242-3. 2001..These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu.. - Cell cycle kinases predicted from conserved biophysical propertiesKazimierz O Wrzeszczynski
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 74:655-68. 2009..An application to the entire human proteome predicted at least 97 human proteins with limited previous annotations to be candidates for cell cycle kinases... - CHOP proteins into structural domain-like fragmentsJinfeng Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
Proteins 55:678-88. 2004..Nevertheless, our results suggested that structural genomics initiatives have to target >30,000 fragments to at least cover the multimember clusters in 62 proteomes... - Membrane protein prediction methodsMarco Punta
Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
Methods 41:460-74. 2007.... - Structural genomics target selection for the New York consortium on membrane protein structureMarco Punta
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY, 10032, USA
J Struct Funct Genomics 10:255-68. 2009..As of December 2008, over 6,000 targets have been selected and are currently being processed by the experimental pipeline. We discuss how our target list may impact structural coverage of the membrane protein space... - Domains, motifs and clusters in the protein universeJinfeng Liu
CUBIC and North East Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Curr Opin Chem Biol 7:5-11. 2003..However, neither automatic nor manual methods are currently entirely up to the challenges of tasks such as target selection in structural genomics. Thus, we urgently need refined and sustained automatic clustering tools... - Prediction in 1D: secondary structure, membrane helices, and accessibilityBurkhard Rost
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Methods Biochem Anal 44:559-87. 2003 - Transmembrane helix predictions revisitedChien Peter Chen
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Protein Sci 11:2774-91. 2002..Overall, by establishing a standardized methodology for transmembrane helix prediction evaluation, we have resolved differences among previous works and presented novel trends that may impact the analysis of entire proteomes... - Sequence conserved for subcellular localizationRajesh Nair
Columbia University Bioinformatics Center (CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Protein Sci 11:2836-47. 2002..We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes... - NORSp: Predictions of long regions without regular secondary structureJinfeng Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3833-5. 2003..It will then return email to the user about the presence and position of disordered regions. NORSp can be accessed from http://cubic.bioc.columbia.edu/services/NORSp/... - Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomesK O Wrzeszczynski
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Cell Mol Life Sci 61:1341-53. 2004..Each experimental annotation yielded, on average, one to three high-accuracy and five to six low-accuracy homology-transfers in the six proteomes. These numbers will increase with each new experimental annotation... - Review: protein secondary structure prediction continues to riseB Rost
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, New York 10032, USA
J Struct Biol 134:204-18. 2001..What is the limit of prediction accuracy? We shall see... - Bioinformatics predictions of localization and targetingShruti Rastogi
Department of Biochemistry and Molecular Biophysics, Columbia University and Columbia University Center for Computational Biology and Bioinformatics C2B2, New York, NY, USA
Methods Mol Biol 619:285-305. 2010..Here, we review some of the most recent methods for the prediction of subcellular localization and protein targeting that contributed toward this breakthrough... - Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to beChristian Schaefer
Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics C2B2, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
Bioinformatics 26:625-31. 2010..Put differently, helices and strands appear to be maintained easily by evolution, whereas maintaining disordered regions appears difficult. Neutral mutations with respect to disorder are therefore very unlikely... - Create and assess protein networks through molecular characteristics of individual proteinsYanay Ofran
Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
Bioinformatics 22:e402-7. 2006..Integrating molecular data and insights about the qualities of individual proteins into the analysis may enhance our ability to decipher biological pathways and processes... - Powerful fusion: PSI-BLAST and consensus sequencesDariusz Przybylski
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Bioinformatics 24:1987-93. 2008..In addition, iterative searches against consensus databases may fail. Here, we addressed these challenges in an attempt to harness the full power of the combination of PSI-BLAST and consensus sequences... - SNAP predicts effect of mutations on protein functionYana Bromberg
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Bioinformatics 24:2397-8. 2008..Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions... - Consensus sequences improve PSI-BLAST through mimicking profile-profile alignmentsDariusz Przybylski
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Nucleic Acids Res 35:2238-46. 2007..We discuss how advanced users of PSI-BLAST can immediately benefit from using consensus sequences on their local computers. We have also made the method available through the Internet (http://www.rostlab.org/services/consensus/)... - Protein-protein interaction hotspots carved into sequencesYanay Ofran
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
PLoS Comput Biol 3:e119. 2007..The server for prediction is available at http://www.rostlab.org/services/isis... - Natively unstructured loops differ from other loopsAvner Schlessinger
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
PLoS Comput Biol 3:e140. 2007..The comparative analysis between NORSnet and DISOPRED2 suggested that long unstructured loops are a major part of unstructured regions in molecular networks... - Improved disorder prediction by combination of orthogonal approachesAvner Schlessinger
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
PLoS ONE 4:e4433. 2009..In sustained cross-validation, MD not only outperforms its origins, but it also compares favorably to other state-of-the-art prediction methods in a variety of tests that we applied. Availability: http://www.rostlab.org/services/md/.. - Comprehensive in silico mutagenesis highlights functionally important residues in proteinsYana Bromberg
Department of Biochemistry Molecular Biophysics, Columbia University, 630 West 168th St, New York, NY 10032, USA
Bioinformatics 24:i207-12. 2008..In vitro mutagenesis is cumbersome and costly: probing all residues in a protein is typically as impossible as substituting by all non-native amino acids. In contrast, such exhaustive mutagenesis is feasible in silico... - Physical protein-protein interactions predicted from microarraysTa Tsen Soong
Columbia University Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
Bioinformatics 24:2608-14. 2008..Predicting physical interactions directly from microarrays is both a challenging and important task that we addressed by developing a novel machine learning method optimized for this task... - SNAP: predict effect of non-synonymous polymorphisms on functionYana Bromberg
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th St, New York, NY 10032, USA
Nucleic Acids Res 35:3823-35. 2007..This measure will allow users to focus on the most accurate predictions and/or the most severe effects. Available at http://www.rostlab.org/services/SNAP... - Epitome: database of structure-inferred antigenic epitopesAvner Schlessinger
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, Room 804, New York, NY 10032, USA
Nucleic Acids Res 34:D777-80. 2006..Interactions can be visualized using an interface to Jmol. The database is available at http://www.rostlab.org/services/epitome/... - LOCnet and LOCtarget: sub-cellular localization for structural genomics targetsRajesh Nair
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 32:W517-21. 2004..The LOCtarget database currently contains localization predictions for all eukaryotic proteins from TargetDB and is updated every week. The server is available at http://www.rostlab.org/services/LOCtarget/... - UniqueProt: Creating representative protein sequence setsSven Mika
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3789-91. 2003..Overall, UniqueProt is a reasonable fast solution for bias in data sets. The service is accessible at http://cubic.bioc.columbia.edu/services/uniqueprot; a command-line version for Linux is downloadable from this web site... - Static benchmarking of membrane helix predictionsAndrew Kernytsky
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3642-4. 2003..An additional feature is that developers can directly investigate any hydrophobicity scale for its potential in predicting membrane helices... - LOC3D: annotate sub-cellular localization for protein structuresRajesh Nair
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3337-40. 2003..The web server can be used to predict sub-cellular localization for proteins for which only a predicted structure is available from threading servers. This makes the resource of particular interest to structural genomics initiatives... - EVA: Evaluation of protein structure prediction serversIngrid Y Y Koh
Columbia University Center for Computational Biology and Bioinformatics C2B2, Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA
Nucleic Acids Res 31:3311-5. 2003..This large sample assures that methods are compared reliably. As a result, EVA provides useful information to developers as well as users of prediction methods... - NLProt: extracting protein names and sequences from papersSven Mika
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 32:W634-7. 2004..bioc.columbia.edu/services/NLProt/). Input can be PubMed/MEDLINE identifiers, authors, titles and journals, as well as collections of abstracts, or entire papers... - DSSPcont: Continuous secondary structure assignments for proteinsPhil Carter
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3293-5. 2003..Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure... - Sequence-based prediction of protein domainsJinfeng Liu
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Nucleic Acids Res 32:3522-30. 2004..Our results appeared to compare favourably with those from previously published methods. CHOPnet may be useful to restrict the experimental testing of different fragments for structure determination in the context of structural genomics... - Predicted protein-protein interaction sites from local sequence informationYanay Ofran
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
FEBS Lett 544:236-9. 2003..Incorporating evolutionary and predicted structural information may improve our method. However, even at this early stage, our tool might already assist wet-lab biology... - Improving fold recognition without foldsDariusz Przybylski
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
J Mol Biol 341:255-69. 2004..If we solved the problem of CPU-time required to apply AGAPE on millions of proteins, our results could also impact everyday database searches... - NMPdb: Database of Nuclear Matrix ProteinsSven Mika
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 33:D160-3. 2005.... - Protein folding rates estimated from contact predictionsMarco Punta
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
J Mol Biol 348:507-12. 2005..The combination of these methods that exploit different sources of information improved performance. It appeared that the combined method reliably distinguished fast from slow two-state folders... - PROFcon: novel prediction of long-range contactsMarco Punta
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University 650 West 168th Street BB217, New York, NY 10032, USA
Bioinformatics 21:2960-8. 2005..While the performance may still be perceived as low, our method clearly pushed the mark higher. Furthermore, predictions are already accurate enough to seed predictions of global features of protein structure... - NLSdb: database of nuclear localization signalsRajesh Nair
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, BB217, 650 West 168th Street, New York, NY 10032, USA
Nucleic Acids Res 31:397-9. 2003..NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. NLSdb can be accessed via the web site: http://cubic.bioc.columbia.edu/db/NLSdb/... - Analysing six types of protein-protein interfacesYanay Ofran
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
J Mol Biol 325:377-87. 2003..Overall, our results suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications... - Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discoveryYanay Ofran
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Drug Discov Today 10:1475-82. 2005..We shall review the challenges, research approaches and recently developed tools in the field of computational function-prediction and we will discuss the ways these issues can change the process of drug discovery... - CAFASP3 in the spotlight of EVAVolker A Eyrich
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 53:548-60. 2003..We challenge that to let machines rule where they are best might be the best way for the community to enjoy the tremendous benefit of CASP as a unique opportunity for brainstorming... - META-PP: single interface to crucial prediction serversVolker A Eyrich
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 31:3308-10. 2003.... - Better prediction of sub-cellular localization by combining evolutionary and structural informationRajesh Nair
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Proteins 53:917-30. 2003..bioc.columbia.edu/db/LOC3D). We imagine that this pilot method-certainly in combination with similar tools-may be valuable target selection in structural genomics... - Critical assessment of methods of protein structure prediction (CASP)--round 6John Moult
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
Proteins 61:3-7. 2005..The article describes the conduct of the experiment and the categories of prediction included, and outlines the evaluation and assessment procedures. A brief summary of progress over the decade of CASP experiments is also provided... - Protein names precisely peeled off free textSven Mika
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
Bioinformatics 20:i241-7. 2004..Here, we introduced a novel system that combines a pre-processing dictionary- and rule-based filtering step with several separately trained support vector machines (SVMs) to identify protein names in the MEDLINE abstracts... - Prediction of DNA-binding residues from sequenceYanay Ofran
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA
Bioinformatics 23:i347-53. 2007..Hence, such studies are not applicable on a large scale. If the 3D structure of a protein is known, it is often possible to predict DNA-binding sites in silico. However, for most proteins, such knowledge is not available... - Natively unstructured regions in proteins identified from contact predictionsAvner Schlessinger
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
Bioinformatics 23:2376-84. 2007..Low propensity for the formation of internal residue contacts has been previously used to predict natively unstructured regions... - MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequenceMarco Lippi
Dipartimento di Sistemi e Informatica, Machine Learning and Neural Networks Group, Universita degli Studi di Firenze, Via di Santa Marta 3, 50139 Firenze, Italy
Bioinformatics 24:2094-5. 2008..8% recall, and at 60.8% precision and 40.7% recall, respectively. AVAILABILITY: Freely available at http://metaldetector.dsi.unifi.it. SUPPLEMENTARY INFORMATION: Details and data can be found at http://metaldetector.dsi.unifi.it/help.php... - Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotesRobert Powers
Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588, USA
Protein Sci 14:2849-61. 2005.... - The protein target list of the Northeast Structural Genomics ConsortiumZeba Wunderlich
Proteins 56:181-7. 2004 - Predicting transmembrane beta-barrels in proteomesHenry R Bigelow
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA
Nucleic Acids Res 32:2566-77. 2004..We challenge that the vast majority of our 164 predictions will eventually be verified experimentally. All proteome predictions and the PROFtmb prediction method are available at http://www.rostlab.org/ services/PROFtmb/... - Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profilesGianluca Pollastri
Department of Information and Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697-3425, USA
Proteins 47:228-35. 2002..SSpro and SSpro8 are implemented as web servers, available together with other structural feature predictors at: http://promoter.ics.uci.edu/BRNN-PRED/...
Research Grants
- Improve predictions of structure and function by PredictProteinBurkhard Rost; Fiscal Year: 2007..The short-term goal is to address two tasks that are closely related to human diseases, namely the distinction between silent and important mutations and the mapping of unstructured proteins onto networks and diseases. ..
- CASP6-CASP8 meetingsBurkhard Rost; Fiscal Year: 2007..CASP also offers an excellent opportunity for training newcomers in sequence analysis. ..
- Comprehensive annotation of subcellular localization of entire organismsBurkhard Rost; Fiscal Year: 2007..g. "expression on ribosomes, bind importin, transport into nucleus, bind DNA, bind exportin, export out of nucleus; next cell cycle". The components proposed here constitute one crucial building block toward such a 4D map of a cell. ..
- Improve predictions of structure and function by PredictProteinBurkhard Rost; Fiscal Year: 2009..The short-term goal is to address two tasks that are closely related to human diseases, namely the distinction between silent and important mutations and the mapping of unstructured proteins onto networks and diseases. ..
- Comprehensive annotation of subcellular localization of entire organismsBurkhard Rost; Fiscal Year: 2009..g. "expression on ribosomes, bind importin, transport into nucleus, bind DNA, bind exportin, export out of nucleus; next cell cycle". The components proposed here constitute one crucial building block toward such a 4D map of a cell. ..
- Improve predictions of structure/function by ProteinBurkhard Rost; Fiscal Year: 2006..As a particular example for using structural information to improve the reliability of inferring function, we propose to investigate the conservation of enzymatic activity. ..
- Predicting putative protein-protein interface segmentsBurkhard Rost; Fiscal Year: 2006..In the best case, we hope to introduce methods that allow automatic discoveries for entire proteomes and considerably help structure prediction. ..
- Intruding into the midnight zone of protein comparisonsBurkhard Rost; Fiscal Year: 2004..However, the particular edge of our method will be to find remote similarities even in the absence of experimental information about structure. ..
- Comprehensive annotation of subcellular localization of entire organismsBurkhard Rost; Fiscal Year: 2010..g. "expression on ribosomes, bind importin, transport into nucleus, bind DNA, bind exportin, export out of nucleus;next cell cycle". The components proposed here constitute one crucial building block toward such a 4D map of a cell. ..