Biochemical Features

The resources in this section include protein identification tools as well as tools which can give you information on the chemical structures and amino acid properties of peptide sequences.

Found 64 links

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AnalyCysDatabase Content

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AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, identification of cysteine residues and disulphide bonds important for folding and stabilization, modeling of protein structures and in protein engineering.

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BioMeTool Content

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Biologically Relevant Metals (BioMe) is a web based platform for calculation of various statistical properties of metal binding sites including distribution of coordinate geometry and other descriptive statistics for a metal ion. The underlying database contains for each metal ion: PDB code, structure determination method, types of metal binding chains and names and coordinates of bound ligands, among other details.

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Calculation of protein isoelectric pointTool Content

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Online estimate of protein isoelectric points. It is highly important to know this parameter for molecular biology analysis, especially in 2D gel electrophoresis and isoelectric focusing. Additionally, there is a short protein isoelectric point calculation manual. You can learn how to write a computer program which will estimate isoelectric point or simply download a ready-made one.

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CAPS-DBDatabase Content

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CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated.

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TitlePublication YearGoogle Scholar Citation Count
CAPS-DB: a structural classification of helix-capping motifs.20120

Cell++Tool Content

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Cell++ is a novel stochastic simulation environment which is capable of modelling diverse biochemical phenomena including signal transduction pathways, metabolic pathways and intracellular calcium signalling.

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Cell++--simulating biochemical pathways200619

CharProtDBDatabase Content

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CharProtDB is a curated database of biochemically characterized proteins. The initial data set in CharProtDB was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.

CHpredictTool Content

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The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.

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CUPSATTool Content

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Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
CUPSAT: prediction of protein stability upon point mutations200695

DEPTHTool Content

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DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

DiANNATool Content

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DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

eBioinformaticsResource Content

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This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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