Nucleic acids research
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
Table of contents
- W1
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EDITORIAL| 2006
- W3
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A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links DirectoryFox, J. A. / McMillan, S. / Ouellette, B. F. et al. | 2006
- W6
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BLAST: improvements for better sequence analysisYe, J. / McGinnis, S. / Madden, T. L. et al. | 2006
- W10
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FISH-family identification of sequence homologues using structure anchored hidden Markov modelsTangrot, J. / Wang, L. / Kagstrom, B. et al. | 2006
- W15
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The MIGenAS integrated bioinformatics toolkit for web-based sequence analysisRampp, M. / Soddemann, T. / Lederer, H. et al. | 2006
- W20
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PAST: fast structure-based searching in the PDBTaubig, H. / Buchner, A. / Griebsch, J. et al. | 2006
- W20
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PreBI: prediction of biological interfaces of proteins in crystalsTsuchiya, Y. / Kinoshita, K. / Ito, N. et al. | 2006
- W24
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oGNM: online computation of structural dynamics using the Gaussian Network ModelYang, L. W. / Rader, A. J. / Liu, X. et al. | 2006
- W32
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PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequenceLi, Z. R. / Lin, H. H. / Han, L. Y. et al. | 2006
- W38
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PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostaticsAzuara, C. / Lindahl, E. / Koehl, P. et al. | 2006
- W43
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PHEPS: web-based pH-dependent Protein Electrostatics ServerKantardjiev, A. A. / Atanasov, B. P. et al. | 2006
- W48
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pKD: re-designing protein pKa valuesTynan-Connolly, B. M. / Nielsen, J. E. et al. | 2006
- W52
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NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysisLindahl, E. / Azuara, C. / Koehl, P. et al. | 2006
- W57
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UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network modelsJang, Y. / Jeong, J. I. / Kim, M. K. et al. | 2006
- W63
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PREDITOR: a web server for predicting protein torsion angle restraintsBerjanskii, M. V. / Neal, S. / Wishart, D. S. et al. | 2006
- W70
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FOLD-RATE: prediction of protein folding rates from amino acid sequenceGromiha, M. M. / Thangakani, A. M. / Selvaraj, S. et al. | 2006
- W75
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Protein Peeling 2: a web server to convert protein structures into series of protein unitsGelly, J. C. / Etchebest, C. / Hazout, S. et al. | 2006
- W79
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ProSAT2-Protein Structure Annotation ServerGabdoulline, R. R. / Ulbrich, S. / Richter, S. et al. | 2006
- W84
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FeatureMap3D-a tool to map protein features and sequence conservation onto homologous structures in the PDBWernersson, R. / Rapacki, K. / Staerfeldt, H. H. et al. | 2006
- W89
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ProKware: integrated software for presenting protein structural properties in protein tertiary structuresHung, J. H. / Huang, H. D. / Lee, T. Y. et al. | 2006
- W95
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OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structuresShih, E. S. / Gan, R. c. / Hwang, M. J. et al. | 2006
- W99
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Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain informationLee, S. / Lee, B. / Jang, I. et al. | 2006
- W104
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TreeDomViewer: a tool for the visualization of phylogeny and protein domain structureAlako, B. T. / Rainey, D. / Nijveen, H. et al. | 2006
- W110
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TreeDet: a web server to explore sequence spaceCarro, A. / Tress, M. / de Juan, D. et al. | 2006
- W116
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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residuesDundas, J. / Ouyang, Z. / Tseng, J. et al. | 2006
- W119
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Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabetTyagi, M. / Sharma, P. / Swamy, C. S. et al. | 2006
- W124
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ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognitionAhmad, S. / Kono, H. / Arauzo-Bravo, M. J. et al. | 2006
- W128
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3dSS: 3D structural superpositionSumathi, K. / Ananthalakshmi, P. / Roshan, M. N. et al. | 2006
- W133
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MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignmentsOzer, H. G. / Ray, W. C. et al. | 2006
- W137
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HHrep: de novo protein repeat detection and the origin of TIM barrelsSoding, J. / Remmert, M. / Biegert, A. et al. | 2006
- W143
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Cascade PSI-BLAST web server: a remote homology search tool for relating protein domainsBhadra, R. / Sandhya, S. / Abhinandan, K. R. et al. | 2006
- W147
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SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon traceMaupetit, J. / Gautier, R. / Tuffery, P. et al. | 2006
- W152
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(PS)2: protein structure prediction serverChen, C. C. / Hwang, J. K. / Yang, J. M. et al. | 2006
- W158
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KemaDom: a web server for domain prediction using kernel machine with local contextChen, L. / Wang, W. / Ling, S. et al. | 2006
- W164
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Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machinesVullo, A. / Bortolami, O. / Pollastri, G. et al. | 2006
- W169
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PONGO: a web server for multiple predictions of all-alpha transmembrane proteinsAmico, M. / Finelli, M. / Rossi, I. et al. | 2006
- W173
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ArchPRED: a template based loop structure prediction serverFernandez-Fuentes, N. / Zhai, J. / Fiser, A. et al. | 2006
- W177
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DISULFIND: a disulfide bonding state and cysteine connectivity prediction serverCeroni, A. / Passerini, A. / Vullo, A. et al. | 2006
- W182
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DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classificationFerre, F. / Clote, P. et al. | 2006
- W186
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PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteinsBigelow, H. / Rost, B. et al. | 2006
- W189
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transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrelsWaldispuhl, J. / Berger, B. / Clote, P. et al. | 2006
- W194
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SVMHC: a server for prediction of MHC-binding peptidesDonnes, P. / Kohlbacher, O. et al. | 2006
- W198
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REMUS: a tool for identification of unique peptide segments as epitopesPai, T. W. / Chang, M. D. / Tzou, W. S. et al. | 2006
- W202
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AlgPred: prediction of allergenic proteins and mapping of IgE epitopesSaha, S. / Raghava, G. P. et al. | 2006
- W210
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pTARGET: a web server for predicting protein subcellular localizationGuda, C. et al. | 2006
- W214
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DOUTfinder-identification of distant domain outliers using subsignificant sequence similarityNovatchkova, M. / Schneider, G. / Fritz, R. et al. | 2006
- W219
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TarFisDock: a web server for identifying drug targets with docking approachLi, H. / Gao, Z. / Kang, L. et al. | 2006
- W225
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sgTarget: a target selection resource for structural genomicsRodrigues, A. P. / Grant, B. J. / Hubbard, R. E. et al. | 2006
- W231
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HARMONY: a server for the assessment of protein structuresPugalenthi, G. / Shameer, K. / Srinivasan, N. et al. | 2006
- W235
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RosettaDesign server for protein designLiu, Y. / Kuhlman, B. et al. | 2006
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CUPSAT: prediction of protein stability upon point mutationsParthiban, V. / Gromiha, M. M. / Schomburg, D. et al. | 2006
- W243
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BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequencesWang, L. / Brown, S. J. et al. | 2006
- W249
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MeMo: a web tool for prediction of protein methylation modificationsChen, H. / Xue, Y. / Huang, N. et al. | 2006
- W254
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SUMOsp: a web server for sumoylation site predictionXue, Y. / Zhou, F. / Fu, C. et al. | 2006
- W258
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MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectraKim, S. / Na, S. / Sim, J. W. et al. | 2006
- W264
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DyNAVacS: an integrative tool for optimized DNA vaccine designHarish, N. / Gupta, R. / Agarwal, P. et al. | 2006
- W267
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NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptidesSouthey, B. R. / Amare, A. / Zimmerman, T. A. et al. | 2006
- W273
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BAGEL: a web-based bacteriocin genome mining toolde Jong, A. / van Hijum, S. A. / Bijlsma, J. J. et al. | 2006
- W280
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GeneAlign: a coding exon prediction tool based on phylogenetical comparisonsHsieh, S. J. / Lin, C. Y. / Liu, N. H. et al. | 2006
- W285
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TOM: a web-based integrated approach for identification of candidate disease genesRossi, S. / Masotti, D. / Nardini, C. et al. | 2006
- W293
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WEGO: a web tool for plotting GO annotationsYe, J. / Fang, L. / Zheng, H. et al. | 2006
- W298
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APID: Agile Protein Interaction DataAnalyzerPrieto, C. / De Las Rivas, J. et al. | 2006
- W303
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Protemot: prediction of protein binding sites with automatically extracted geometrical templatesChang, D. T. / Weng, Y. Z. / Lin, J. H. et al. | 2006
- W310
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GRAMM-X public web server for protein-protein dockingTovchigrechko, A. / Vakser, I. A. et al. | 2006
- W315
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TSEMA: interactive prediction of protein pairings between interacting familiesIzarzugaza, J. M. / Juan, D. / Pons, C. et al. | 2006
- W325
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kinDOCK: a tool for comparative docking of protein kinase ligandsMartin, L. / Catherinot, V. / Labesse, G. et al. | 2006
- W330
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YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology termsPenkett, C. J. / Morris, J. A. / Wood, V. et al. | 2006
- W335
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The MPI Bioinformatics Toolkit for protein sequence analysisBiegert, A. / Mayer, C. / Remmert, M. et al. | 2006
- W340
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VIRGO: computational prediction of gene functionsMassjouni, N. / Rivera, C. G. / Murali, T. M. et al. | 2006
- W345
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TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDBYamasaki, C. / Kawashima, H. / Todokoro, F. et al. | 2006
- W350
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DILIMOT: discovery of linear motifs in proteinsNeduva, V. / Russell, R. B. et al. | 2006
- W356
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MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequencesHsu, C. M. / Chen, C. Y. / Liu, B. J. et al. | 2006
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ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteinsde Castro, E. / Sigrist, C. J. / Gattiker, A. et al. | 2006
- W366
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MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomesNeph, S. / Tompa, M. et al. | 2006
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MEME: discovering and analyzing DNA and protein sequence motifsBailey, T. L. / Williams, N. / Misleh, C. et al. | 2006
- W374
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HHsenser: exhaustive transitive profile search using HMM-HMM comparisonSoding, J. / Remmert, M. / Biegert, A. et al. | 2006
- W379
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JAFA: a protein function annotation meta-serverFriedberg, I. / Harder, T. / Godzik, A. et al. | 2006
- W382
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SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysisLiang, H. / Zhou, W. / Landweber, L. F. et al. | 2006
- W385
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Virtual Ribosome-a comprehensive DNA translation tool with support for integration of sequence feature annotationWernersson, R. et al. | 2006
- W389
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GenDecoder: genetic code prediction for metazoan mitochondriaAbascal, F. / Zardoya, R. / Posada, D. et al. | 2006
- W394
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NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genesDeSantis, T. Z. / Hugenholtz, P. / Keller, K. et al. | 2006
- W400
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CrossLink: visualization and exploration of sequence relationships between (micro) RNAsDezulian, T. / Schaefer, M. / Wiese, R. et al. | 2006
- W405
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CorreLogo: an online server for 3D sequence logos of RNA and DNA alignmentsBindewald, E. / Schneider, T. D. / Shapiro, B. A. et al. | 2006
- W412
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The ARTS web server for aligning RNA tertiary structuresDror, O. / Nussinov, R. / Wolfson, H. J. et al. | 2006
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PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structuresByun, Y. / Han, K. et al. | 2006
- W423
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RNAMST: efficient and flexible approach for identifying RNA structural homologsChang, T. H. / Huang, H. D. / Chuang, T. N. et al. | 2006
- W429
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RegRNA: an integrated web server for identifying regulatory RNA motifs and elementsHuang, H. Y. / Chien, C. H. / Jen, K. H. et al. | 2006
- W435
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AUGUSTUS: ab initio prediction of alternative transcriptsStanke, M. / Keller, O. / Gunduz, I. et al. | 2006
- W440
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ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterizationCastrignano, T. / Rizzi, R. / Talamo, I. G. et al. | 2006
- W444
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ASGS: an alternative splicing graph web serviceBollina, D. / Lee, B. T. / Tan, T. W. et al. | 2006
- W448
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siVirus: web-based antiviral siRNA design software for highly divergent viral sequencesNaito, Y. / Ui-Tei, K. / Nishikawa, T. et al. | 2006
- W451
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RNAhybrid: microRNA target prediction easy, fast and flexibleKruger, J. / Rehmsmeier, M. et al. | 2006
- W455
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ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAsNam, J. W. / Kim, J. / Kim, S. K. et al. | 2006
- W459
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EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragmentsMasoudi-Nejad, A. / Tonomura, K. / Kawashima, S. et al. | 2006
- W463
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jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1Zhang, M. / Schultz, A. K. / Calef, C. et al. | 2006
- W466
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BiologicalNetworks: visualization and analysis tool for systems biologyBaitaluk, M. / Sedova, M. / Ray, A. et al. | 2006
- W472
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BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experimentsAl-Shahrour, F. / Minguez, P. / Tarraga, J. et al. | 2006
- W477
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CAPweb: a bioinformatics CGH array Analysis PlatformLiva, S. / Hupe, P. / Neuvial, P. et al. | 2006
- W482
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BTW: a web server for Boltzmann time warping of gene expression time seriesFerre, F. / Clote, P. et al. | 2006
- W486
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Next station in microarray data analysis: GEPASMontaner, D. / Tarraga, J. / Huerta-Cepas, J. et al. | 2006
- W492
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GEPS: the Gene Expression Pattern ScannerWang, Y. P. / Liang, L. / Han, B. C. et al. | 2006
- W498
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CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysisRainer, J. / Sanchez-Cabo, F. / Stocker, G. et al. | 2006
- W504
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Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysisManfield, I. W. / Jen, C. H. / Pinney, J. W. et al. | 2006
- W510
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JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology informationScheer, M. / Klawonn, F. / Munch, R. et al. | 2006
- W516
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Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleasesMandell, J. G. / Barbas, C. F. et al. | 2006
- W524
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TFBScluster web server for the identification of mammalian composite regulatory elementsDonaldson, I. J. / Gottgens, B. et al. | 2006
- W529
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VOMBAT: prediction of transcription factor binding sites using variable order Bayesian treesGrau, J. / Ben-Gal, I. / Posch, S. et al. | 2006
- W534
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POXO: a web-enabled tool series to discover transcription factor binding sitesKankainen, M. / Pehkonen, P. / Rosenstom, P. et al. | 2006
- W541
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Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithmWaleev, T. / Shtokalo, D. / Konovalova, T. et al. | 2006
- W546
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jPREdictor: a versatile tool for the prediction of cis-regulatory elementsFiedler, T. / Rehmsmeier, M. et al. | 2006
- W551
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CEAS: cis-regulatory element annotation systemJi, X. / Li, W. / Song, J. et al. | 2006
- W555
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Stubb: a program for discovery and analysis of cis-regulatory modulesSinha, S. / Liang, Y. / Siggia, E. et al. | 2006
- W560
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NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factorsLuykx, P. / Bajic, I. V. / Khuri, S. et al. | 2006
- W566
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MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genesPavesi, G. / Mereghetti, P. / Zambelli, F. et al. | 2006
- W571
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CRSD: a comprehensive web server for composite regulatory signature discoveryLiu, C. C. / Lin, C. C. / Chen, W. S. et al. | 2006
- W578
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PromAn: an integrated knowledge-based web server dedicated to promoter analysisLardenois, A. / Chalmel, F. / Bianchetti, L. et al. | 2006
- W584
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iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic speciesRanjan, S. / Seshadri, J. / Vindal, V. et al. | 2006
- W588
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TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sitesTech, M. / Morgenstern, B. / Meinicke, P. et al. | 2006
- W591
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FeatureScan: revealing property-dependent similarity of nucleotide sequencesDeyneko, I. V. / Bredohl, B. / Wesely, D. et al. | 2006
- W596
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Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignmentLassmann, T. / Sonnhammer, E. L. et al. | 2006
- W600
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PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignmentsMoretti, S. / Reinier, F. / Poirot, O. et al. | 2006
- W604
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Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-CoffeeArmougom, F. / Moretti, S. / Poirot, O. et al. | 2006
- W609
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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsSuyama, M. / Torrents, D. / Bork, P. et al. | 2006
- W613
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AliWABA: alignment on the web through an A-Bruijn approachJones, N. C. / Zhi, D. / Raphael, B. J. et al. | 2006
- W617
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FootPrinter3: phylogenetic footprinting in partially alignable sequencesFang, F. / Blanchette, M. et al. | 2006
- W621
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PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposesConde, L. / Vaquerizas, J. M. / Dopazo, H. et al. | 2006
- W626
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New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-TranslateKhatri, P. / Desai, V. / Tarca, A. L. et al. | 2006
- W632
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PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNACasillas, S. / Barbadilla, A. et al. | 2006
- W635
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FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritizationYuan, H. Y. / Chiou, J. J. / Tseng, W. H. et al. | 2006
- W642
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SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequencesHan, A. / Kang, H. J. / Cho, Y. et al. | 2006
- W651
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SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomesAndreson, R. / Puurand, T. / Remm, M. et al. | 2006
- W656
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SSRPrimer and SSR Taxonomy Tree: Biome SSR discoveryJewell, E. / Robinson, A. / Savage, D. et al. | 2006
- W660
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MutScreener: primer design tool for PCR-direct sequencingYao, F. / Zhang, R. / Zhu, Z. et al. | 2006
- W665
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PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genomeYamada, T. / Soma, H. / Morishita, S. et al. | 2006
- W670
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GeMprospector-online design of cross-species genetic marker candidates in legumes and grassesFredslund, J. / Madsen, L. H. / Hougaard, B. K. et al. | 2006
- W676
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QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequencesKikin, O. / D'Antonio, L. / Bagga, P. S. et al. | 2006
- W683
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Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequencesScaria, V. / Hariharan, M. / Arora, A. et al. | 2006
- W686
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GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequencesGao, F. / Zhang, C. T. et al. | 2006
- W692
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CorGen-measuring and generating long-range correlations for DNA sequence analysisMesser, P. W. / Arndt, P. F. et al. | 2006
- W696
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SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchangesLin, Y. C. / Lu, C. L. / Liu, Y. C. et al. | 2006
- W700
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ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution onlinePosada, D. et al. | 2006
- W704
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The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analysesSchultz, J. / Muller, T. / Achtziger, M. et al. | 2006
- W708
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PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeatsToth, G. / Deak, G. / Barta, E. et al. | 2006
- W714
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The Path-A metabolic pathway prediction web serverPireddu, L. / Szafron, D. / Lu, P. et al. | 2006
- W720
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KOBAS server: a web-based platform for automated annotation and pathway identificationWu, J. / Mao, X. / Cai, T. et al. | 2006
- W725
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metaSHARK: a WWW platform for interactive exploration of metabolic networksHyland, C. / Pinney, J. W. / McConkey, G. A. et al. | 2006
- W729
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Taverna: a tool for building and running workflows of servicesHull, D. / Wolstencroft, K. / Stevens, R. et al. | 2006
- W733
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GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interfaceLo, A. / Stenutz, R. / Schwarzer, E. et al. | 2006
- W738
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FAF-Drugs: free ADME/tox filtering of compound collectionsMiteva, M. A. / Violas, S. / Montes, M. et al. | 2006
- W745
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HubMed: a web-based biomedical literature search interfaceEaton, A. D. et al. | 2006
- W748
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botXminer: mining biomedical literature with a new web-based applicationMudunuri, U. / Stephens, R. / Bruining, D. et al. | 2006