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Related Links for GlyNest and CASPERTool Content

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AS2TSTool Content

http://as2ts.llnl.gov/ [open in a new window]

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Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction

The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.

links directory index: 410
TitlePublication YearGoogle Scholar Citation Count
AS2TS system for protein structure modeling and analysis200524
LGA: A method for finding 3D similarities in protein structures2003386
NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsalgorithms biomolecular nuclear magnetic resonance proteins sequence alignment

Bioinformatics Links DirectoryResource Content

http://www.bioinformatics.ca/links_directory/ [open in a new window]

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Education > Directories and Portals

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

This content is being maintained by Francis Ouellette.

links directory index: 124
TitlePublication YearGoogle Scholar Citation Count
Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory201010
Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory200914
Keeping pace with the data: 2008 update on the Bioinformatics Links Directory200816
Conducting research on the web: 2007 update for the bioinformatics links directory200723
A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory200629
The Bioinformatics Links Directory: a compilation of molecular biology web servers200532
NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2005NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2008NAR Web Server Issue 2009NAR Web Server Issue 2010NAR Web Server Issue 2011NAR Web Server Issue 2012
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external linksLink on Twitter Link on Wikipedia

CS23DTool Content

http://www.cs23d.ca [open in a new window]

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Protein > 3-D Structure Prediction

Chemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.

links directory index: 76
TitlePublication YearGoogle Scholar Citation Count
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data200876
NAR Web Server Issue 2008
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DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp [open in a new window]

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DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

links directory index: 3468
TitlePublication YearGoogle Scholar Citation Count
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists2007161
DAVID: Database for Annotation, Visualization, and Integrated Discovery20033307
NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

GlycoFragmentTool Content

http://www.glycosciences.de/tools/GlycoFragments/fragment.php4 [open in a new window]

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Other Molecules > Carbohydrates

GlycoFragment is a tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.

This content is being maintained by luetteke.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates200441
NAR Web Server Issue 2004
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GlycomeDBDatabase Content

http://www.glycome-db.org [open in a new window]

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Other Molecules > Carbohydrates
Other Molecules > Databases

GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank. The database is a unified resource for carbohydrate structures. GlycomeDB retains the links to the original databases and is updated at weekly intervals with the newest structures available from the source databases.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
GlycomeDB--a unified database for carbohydrate structures20112
NAR Database Issue 2011
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external linksLink on Wikipedia
tagscarbohydrate sequence carbohydrates factual databases glycomics systems integration

Glycosciences.deResource Content

http://www.glycosciences.de [open in a new window]

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Other Molecules > Carbohydrates

The glycosciences.de web portal provides a series of tools and databases related to glycobiology and glycomics.

This content is being maintained by luetteke.

links directory index: 86
TitlePublication YearGoogle Scholar Citation Count
GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research200686
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tagsapplications carbohydrate conformation carbohydrates computational biology data collection databases factual databases glycobiology glycoconjugates glycoinformatics glycomics glycoproteins humans polysaccharides research

GlycoSearchMSTool Content

http://www.glycosciences.de/sweetdb/start.php?action=form_ms_search [open in a new window]

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Other Molecules > Carbohydrates

GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.

This content is being maintained by luetteke.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates200441
NAR Web Server Issue 2004
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tagsalgorithms carbohydrate sequence humans mass spectrometry polysaccharides

GlycoViewerTool Content

http://www.systemsbiology.org.au/glycoviewer [open in a new window]

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Other Molecules > Carbohydrates

The GlycoViewer is a web-based tool that can visualize, summarize and compare sets of gylcan structures.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
GlycoViewer: a tool for visual summary and comparative analysis of the glycome20101
NAR Web Server Issue 2010
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tagsglycomics glycoproteins humans neoplasms polysaccharides

HMDBDatabase Content

http://www.hmdb.ca/ [open in a new window]

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Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

links directory index: 73
TitlePublication YearGoogle Scholar Citation Count
Metabolomics: the principles and potential applications to transplantation200573
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external linksLink on Wikipedia
tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance factual databases humans internet magnetic resonance spectroscopy mass spectrometry metabolic diseases metabolic networks and pathways metabolism metabolome organ transplantation quality control user-computer interface

HubMedTool Content

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

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Literature > Search Tools

HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
HubMed: a web-based biomedical literature search interface200639
NAR Web Server Issue 2006
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external linksLink on Wikipedia
tagspubmed systems integration

IMGT/3DstructureDatabase Content

http://www.imgt.org/3Dstructure-DB/ [open in a new window]

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Protein > Databases

IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system for immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin and MHC superfamilies (IgSF and MhcSF, respectively) and found in complexes with IG, TR or MHC. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY concepts and axioms. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. In its Web version, the IMGT/DomainGapAlign tool analyses amino acid sequences, per domain.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF201033
NAR Database Issue 2010
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tagsalleles amino acid sequence amino acid sequence homology animals antigen receptors computational biology genetic databases humans immunoglobulins major histocompatibility complex molecular sequence data protein databases tertiary protein structure

LGATool Content

http://proteinmodel.org/AS2TS/LGA/lga.html [open in a new window]

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Protein > 3-D Structure Comparison

Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.

links directory index: 386
TitlePublication YearGoogle Scholar Citation Count
LGA: A method for finding 3D similarities in protein structures2003386
NAR Web Server Issue 2003
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Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/ [open in a new window]

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Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

links directory index: 343
TitlePublication YearGoogle Scholar Citation Count
Mimicking cellular sorting improves prediction of subcellular localization2005234
Better prediction of sub-cellular localization by combining evolutionary and structural information200376
LOC3D: annotate sub-cellular localization for protein structures200333
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

NMR Constraints AnalyserTool Content

http://molsim.sci.univr.it/constraint [open in a new window]

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Protein > 3-D Structure Prediction

NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.20102
NAR Web Server Issue 2010
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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation

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