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NAR Web Server Issue 2003

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Found 117 links

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ClustalWTool Content

http://www.ebi.ac.uk/clustalw/ [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

Standard multiple sequence alignment.

links directory index: 43452
TitlePublication YearGoogle Scholar Citation Count
Multiple sequence alignment with the Clustal series of programs20032994
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice199440458
NAR Web Server Issue 2003
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Swiss ModelTool Content

http://www.expasy.ch/swissmod/SWISS-MODEL.html [open in a new window]

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Protein > 3-D Structure Prediction

Automated protein modelling server.

links directory index: 11411
TitlePublication YearGoogle Scholar Citation Count
The SWISS-MODEL Repository: new features and functionalities200681
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling20061560
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models2004229
SWISS-MODEL: An automated protein homology-modeling server20032847
Large scale protein modelling and model repository199726
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling19976668
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence automation chemical models computational biology computer simulation factual databases genome humans molecular models molecular sequence data online systems protein conformation protein databases protein sequence analysis protein structural homology proteins reproducibility of results sequence alignment switzerland systems integration

ModellerTool Content

http://salilab.org/modeller/ [open in a new window]

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Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

links directory index: 8225
TitlePublication YearGoogle Scholar Citation Count
Modeller: generation and refinement of homology-based protein structure models2003437
Tools for comparative protein structure modeling and analysis2003190
Modeling of loops in protein structures2000826
Comparative protein structure modeling of genes and genomes20001572
Comparative protein modelling by satisfaction of spatial restraints19935200
NAR Web Server Issue 2003
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MfoldTool Content

http://mfold.rna.albany.edu/?q=mfold/download-mfold [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.

links directory index: 5095
TitlePublication YearGoogle Scholar Citation Count
Mfold web server for nucleic acid folding and hybridization prediction20034923
Prediction of RNA secondary structure by energy minimization1994172
NAR Web Server Issue 2003
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T-COFFEETool Content

http://www.tcoffee.org/ [open in a new window]

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The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

links directory index: 4274
TitlePublication YearGoogle Scholar Citation Count
R-Coffee: a web server for accurately aligning noncoding RNA sequences200817
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods200768
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments200615
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
3DCoffee: combining protein sequences and structures within multiple sequence alignments2004222
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment2004121
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments2003201
T-Coffee: A novel method for fast and accurate multiple sequence alignment20003173
COFFEE: an objective function for multiple sequence alignments1998183
NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence databases as topic dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans information storage and retrieval internet messenger rna molecular sequence data nucleic acid conformation phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment software untranslated rna user-computer interface

PSORT.orgTool Content

http://www.psort.org/ [open in a new window]

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Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

links directory index: 3330
TitlePublication YearGoogle Scholar Citation Count
PSORTdb: a protein subcellular localization database for bacteria2005101
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria2003292
Extensive feature detection of N-terminal protein sorting signals2002414
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization19991544
Better prediction of protein cellular localization sites with the k nearest neighbors classifier1997395
Expert system for predicting protein localization sites in gram-negative bacteria1991584
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

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links directory index: 3142
TitlePublication YearGoogle Scholar Citation Count
The Gibbs Centroid Sampler200735
Decoding human regulatory circuits200493
Gibbs Recursive Sampler: finding transcription factor binding sites2003260
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes2001225
Human-mouse genome comparisons to locate regulatory sites2000454
Gibbs motif sampling: detection of bacterial outer membrane protein repeats1995392
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment19931683
NAR Web Server Issue 2003NAR Web Server Issue 2007
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SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

links directory index: 2017
TitlePublication YearGoogle Scholar Citation Count
SIFT: Predicting amino acid changes that affect protein function2003960
Accounting for human polymorphisms predicted to affect protein function2002394
Predicting deleterious amino acid substitutions2001663
NAR Web Server Issue 2003
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ESPriptTool Content

http://espript.ibcp.fr/ESPript/ESPript/index.php [open in a new window]

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Sequence Comparison > Alignment Editing and Visualization

Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.

links directory index: 2009
TitlePublication YearGoogle Scholar Citation Count
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins2003415
ESPript: analysis of multiple sequence alignments in PostScript19991594
NAR Web Server Issue 2003
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Institute of Enzymology ServersTool Content

http://www.enzim.hu/index.php?option=com_content&task=blogcategory&id=30&Itemid=... [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.

links directory index: 2004
TitlePublication YearGoogle Scholar Citation Count
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates200546
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content2005392
The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins2005235
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes200552
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank2005138
Transmembrane proteins in the Protein Data Bank: identification and classification2004138
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation200443
SCide: identification of stabilization centers in proteins.20030
Servers for sequence-structure relationship analysis and prediction20035
On filtering false positive transmembrane protein predictions200257
The HMMTOP transmembrane topology prediction server.20010
Principles governing amino acid composition of integral membrane proteins: application to topology prediction1998795
Stabilization centers in proteins: identification, characterization and predictions1997103
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acids binding sites capsid proteins cell line chemical models computational biology computer simulation conserved sequence cysteine database management systems dna methylation dna primers drug stability energy transfer genome genomics humans hydrophobic and hydrophilic interactions kringles lipid bilayers markov chains membrane proteins molecular models molecular sequence data neural networks (computer) oxidation-reduction pliability polymerase chain reaction protein binding protein conformation protein databases protein engineering protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment statistical models structure-activity relationship sulfites temperature tertiary protein structure thermodynamics tissue plasminogen activator

ScansiteTool Content

http://scansite.mit.edu/ [open in a new window]

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Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

links directory index: 1698
TitlePublication YearGoogle Scholar Citation Count
Computational prediction of protein-protein interactions200432
Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs2003825
A motif-based profile scanning approach for genome-wide prediction of signaling pathways2001418
Use of an oriented peptide library to determine the optimal substrates of protein kinases1994423
NAR Web Server Issue 2003
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CASTpTool Content

http://sts.bioengr.uic.edu/castp/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

links directory index: 1616
TitlePublication YearGoogle Scholar Citation Count
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues2006372
CASTp: Computed Atlas of Surface Topography of proteins2003264
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins1998153
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape1998226
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design1998601
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/ [open in a new window]

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Education > Directories and Portals
Protein > Do-it-all Tools for Protein

ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

links directory index: 1342
TitlePublication YearGoogle Scholar Citation Count
ExPASy: The proteomics server for in-depth protein knowledge and analysis20031342
NAR Web Server Issue 2003NAR Web Server Issue 2012
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tagsenzymes gel electrophoresis internet molecular models protein conformation protein databases protein sequence analysis proteins proteomics software systems integration user-computer interface

RSATTool Content

http://rsat.ccb.sickkids.ca/ [open in a new window]

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DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

links directory index: 1280
TitlePublication YearGoogle Scholar Citation Count
RSAT: regulatory sequence analysis tools2008115
Regulatory sequence analysis tools2003299
A web site for the computational analysis of yeast regulatory sequences2000179
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies1998687
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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/ [open in a new window]

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RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

links directory index: 1276
TitlePublication YearGoogle Scholar Citation Count
Tools for the automatic identification and classification of RNA base pairs2003125
Geometric nomenclature and classification of RNA base pairs2001373
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids1992778
NAR Web Server Issue 2003
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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

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