Small Molecules, Immunoglobulins

Tools for dealing with the bioinformatics of small molecules and immunoglobulins.

Found 30 links

Displaying 15 links

ARISTOTool Content

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Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

CFM-IDTool Content

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CFM-ID (Competitive Fragmentation Modeling) is a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra data.

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ChemMine ToolsTool Content

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ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

DrugBankDatabase Content

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DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14,000 protein or drug target sequences are linked to these drug entries.

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eMoleculesDatabase Content

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eMolecules is a search engine for chemical structures that allows for substructure searching.

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FAF-DrugsTool Content

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Free ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
FAF-Drugs: free ADME/tox filtering of compound collections200639

FpocketTool Content

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Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

FrogTool Content

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Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).

links directory index: 32
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Frog: a FRee Online druG 3D conformation generator200732

Frog2Tool Content

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Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

IC50-to-KiTool Content

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A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

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idTargetTool Content

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idTarget is a web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. idTarget screens against protein structures in PDB.

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IgBLASTTool Content

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IgBLAST web tool can be used to view the matches to germline V(D)J gene segments, details at rearrangement junctions, the delineation of Ig sub-regions as well as other commonly sought information. IgBLAST has the capacity to analyze both nucleotide and protein sequences.

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LISETool Content

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LISE is a web server for a novel method of predicting small molecule binding sites on proteins.

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MBRoleResource Content

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Metabolite Biological Role (MBRole) is a web server for carrying out over-representation analysis of biological and chemical annotations in arbitrary sets of metabolites (small chemical compounds) coming from metabolomic data of any organism or sample. MBRole performs enrichment analysis of categorical annotations for a set of compounds of interest. These categorical annotations correspond to biological and chemical information available in a number of public databases and software.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
MBRole: enrichment analysis of metabolomic data20114

MoMA-LigPathTool Content

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MoMA-LigPath is a web server for simulating protein-ligand unbinding. It computes the ligand exit path from the active site to the protein surface using robotics-inspired algorithms. The PDB file provided as input may contain several ligands.

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