《核酸研究》.2006年.第We期

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• KemaDom: a web server for domain prediction using kernel machine with
• PROFtmb: a web server for predicting bacterial transmembrane beta barr
• DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine
• transFold: a web server for predicting the structure and residue conta
• REMUS: a tool for identification of unique peptide segments as epitope
• AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
• SVMHC: a server for prediction of MHC-binding peptides
• TarFisDock: a web server for identifying drug targets with docking app
• sgTarget: a target selection resource for structural genomics
• CUPSAT: prediction of protein stability upon point mutations
• SUMOsp: a web server for sumoylation site prediction
• RosettaDesign server for protein design
• BindN: a web-based tool for efficient prediction of DNA and RNA bindin
• RosettaDesign server for protein design
• RosettaDesign server for protein design
• TOM: a web-based integrated approach for identification of candidate d
• GeneAlign: a coding exon prediction tool based on phylogenetical compa
• Protemot: prediction of protein binding sites with automatically extra
• Next station in microarray data analysis: GEPAS
• Arabidopsis Co-expression Tool(ACT): web server tools for microarray-
• GEPS: the Gene Expression Pattern Scanner
• CARMAweb: comprehensive R- and bioconductor-based web service for micr
• VOMBAT: prediction of transcription factor binding sites using variabl
• CorreLogo: an online server for 3D sequence logos of RNA and DNA align
• CrossLink: visualization and exploration of sequence relationships bet
• NAST: a multiple sequence alignment server for comparative analysis of
• RNAMST: efficient and flexible approach for identifying RNA structural
• PseudoViewer: web application and web service for visualizing RNA pseu
• AUGUSTUS: ab initio prediction of alternative transcripts
• RegRNA: an integrated web server for identifying regulatory RNA motifs
• siVirus: web-based antiviral siRNA design software for highly divergen
• ASGS: an alternative splicing graph web service
• ASPIC: a web resource for alternative splicing prediction and transcri
• ProMiR II: a web server for the probabilistic prediction of clustered,
• RNAhybrid: microRNA target prediction easy, fast and flexible
• BiologicalNetworks: visualization and analysis tool for systems biolog
• EGassembler: online bioinformatics service for large-scale processing,
• BTW: a web server for Boltzmann time warping of gene expression time s
• CAPweb: a bioinformatics CGH array Analysis Platform
• BABELOMICS: a systems biology perspective in the functional annotation
• TSEMA: interactive prediction of protein pairings between interacting
• VIRGO: computational prediction of gene functions
• The MPI Bioinformatics Toolkit for protein sequence analysis
• HHsenser: exhaustive transitive profile search using HMM–HMM compariso
• MEME: discovering and analyzing DNA and protein sequence motifs
• SWAKK: a web server for detecting positive selection in proteins using
• SWAKK: a web server for detecting positive selection in proteins using
• JAFA: a protein function annotation meta-server
• GenDecoder: genetic code prediction for metazoan mitochondria
• Virtual Ribosome—a comprehensive DNA translation tool with support for
• GRAMM-X public web server for protein–protein docking
• YOGY: a web-based, integrated database to retrieve protein orthologs a
• kinDOCK: a tool for comparative docking of protein kinase ligands
• PREDITOR: a web server for predicting protein torsion angle restraints
• UMMS: constrained harmonic and anharmonic analyses of macromolecules b
• ReadOut: structure-based calculation of direct and indirect readout en
• Cascade PSI-BLAST web server: a remote homology search tool for relati
• Cascade PSI-BLAST web server: a remote homology search tool for relati
• Spritz: a server for the prediction of intrinsically disordered region
• PONGO: a web server for multiple predictions of all-alpha transmembran
• DISULFIND: a disulfide bonding state and cysteine connectivity predict
• ArchPRED: a template based loop structure prediction server
• AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
• TarFisDock: a web server for identifying drug targets with docking app
• pTARGET: a web server for predicting protein subcellular localization
• DOUTfinder—identification of distant domain outliers using subsignific
• pTARGET: a web server for predicting protein subcellular localization
• HARMONY: a server for the assessment of protein structures
• MODi : a powerful and convenient web server for identifying multiple p
• SUMOsp: a web server for sumoylation site prediction
• MeMo: a web tool for prediction of protein methylation modifications
• BAGEL: a web-based bacteriocin genome mining tool
• NeuroPred: a tool to predict cleavage sites in neuropeptide precursors
• DyNAVacS: an integrative tool for optimized DNA vaccine design
• APID: Agile Protein Interaction DataAnalyzer
• WEGO: a web tool for plotting GO annotations
• EDITORIAL
• FISH—family identification of sequence homologues using structure anch
• BLAST: improvements for better sequence analysis
• A compilation of molecular biology web servers: 2006 update on the Bio
• PAST: fast structure-based searching in the PDB
• PreBI: prediction of biological interfaces of proteins in crystals
• The MIGenAS integrated bioinformatics toolkit for web-based sequence a
• PROFEAT: a web server for computing structural and physicochemical fea
• oGNM: online computation of structural dynamics using the Gaussian Net
• NOMAD-Ref: visualization, deformation and refinement of macromolecular
• pKD: re-designing protein pKa values
• PHEPS: web-based pH-dependent Protein Electrostatics Server
• PDB_Hydro: incorporating dipolar solvents with variable density in the
• ProSAT2—Protein Structure Annotation Server
• Protein Peeling 2: a web server to convert protein structures into ser
• FOLD-RATE: prediction of protein folding rates from amino acid sequenc
• ProKware: integrated software for presenting protein structural proper
• FeatureMap3D—a tool to map protein features and sequence conservation
• TreeDomViewer: a tool for the visualization of phylogeny and protein d
• Localizome: a server for identifying transmembrane topologies and TM h
• OPAAS: a web server for optimal, permuted, and other alternative align
• CASTp: computed atlas of surface topography of proteins with structura
• TreeDet: a web server to explore sequence space
• Protein Block Expert(PBE): a web-based protein structure analysis ser
• MAVL/StickWRLD: analyzing structural constraints using interpositional
• HHrep: de novo protein repeat detection and the origin of TIM barrels
• 3dSS: 3D structural superposition
• (PS)2: protein structure prediction server
• SABBAC: online Structural Alphabet-based protein BackBone reconstructi
• MAGIIC-PRO: detecting functional signatures by efficient discovery of
• DILIMOT: discovery of linear motifs in proteins
• TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
• MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic
• ScanProsite: detection of PROSITE signature matches and ProRule-associ
• The ARTS web server for aligning RNA tertiary structures
• jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-
• TFBScluster web server for the identification of mammalian composite r
• CRSD: a comprehensive web server for composite regulatory signature di
• MoD Tools: regulatory motif discovery in nucleotide sequences from co-
• FeatureScan: revealing property-dependent similarity of nucleotide seq
• TICO: a tool for postprocessing the predictions of prokaryotic transla
• iCR: a web tool to identify conserved targets of a regulatory protein
• PAL2NAL: robust conversion of protein sequence alignments into the cor
• SNPmasker: automatic masking of SNPs and repeats across eukaryotic gen
• Applications for protein sequence–function evolution data: mRNA/protei
• SNP@Domain: a web resource of single nucleotide polymorphisms(SNPs) w
• PrimerStation: a highly specific multiplex genomic PCR primer design s
• MutScreener: primer design tool for PCR-direct sequencing
• SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
• HubMed: a web-based biomedical literature search interface
• FAF-Drugs: free ADME/tox filtering of compound collections
• GlyNest and CASPER: two independent approaches to estimate 1H and 13C
• botXminer: mining biomedical literature with a new web-based applicati
• New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate
• Quadfinder: server for identification and analysis of quadruplex-formi
• QGRS Mapper: a web-based server for predicting G-quadruplexes in nucle
• GeMprospector—online design of cross-species genetic marker candidates
• SPRING: a tool for the analysis of genome rearrangement using reversal
• CorGen—measuring and generating long-range correlations for DNA sequen
• GC-Profile: a web-based tool for visualizing and analyzing the variati
• The Path-A metabolic pathway prediction web server
• PLOTREP: a web tool for defragmentation and visual analysis of dispers
• The internal transcribed spacer 2 database—a web server for(not only)
• ModelTest Server: a web-based tool for the statistical selection of mo
• Taverna: a tool for building and running workflows of services
• Zinc Finger Tools: custom DNA-binding domains for transcription factor
• JProGO: a novel tool for the functional interpretation of prokaryotic
• jPREdictor: a versatile tool for the prediction of cis-regulatory elem
• Composite Module Analyst: identification of transcription factor bindi
• POXO: a web-enabled tool series to discover transcription factor bindi
• NXSensor web tool for evaluating DNA for nucleosome exclusion sequence
• Stubb: a program for discovery and analysis of cis-regulatory modules
• CEAS: cis-regulatory element annotation system
• PromAn: an integrated knowledge-based web server dedicated to promoter
• Expresso: automatic incorporation of structural information in multipl
• PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide
• Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignmen
• PupaSuite: finding functional single nucleotide polymorphisms for larg
• FootPrinter3: phylogenetic footprinting in partially alignable sequenc
• AliWABA: alignment on the web through an A-Bruijn approach
• FASTSNP: an always up-to-date and extendable service for SNP function
• PDA v.2: improving the exploration and estimation of nucleotide polymo
• metaSHARK: a WWW platform for interactive exploration of metabolic net
• KOBAS server: a web-based platform for automated annotation and pathwa