> > Biochemical Features

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.

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Found 63 links

Displaying 15 links

AnalyCysDatabase Content

http://bioinformatics.univ-reunion.fr/analycys/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

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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Ar_NHPredTool Content

http://www.imtech.res.in/raghava/ar_nhpred [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes
Protein > Sequence Features

The Ar_NHPred server predicts the aromatic backbone NH interaction in a given amino acid sequence where the pi ring of aromatic residues interact with the backbone NH groups.

This content is being maintained by raghavagps.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
Role of evolutionary information in prediction of aromatic-backbone NH interactions in proteins20044
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tagsaromatic amino acids aromatic-backbone hydrogen bonding molecular evolution molecular models multiple sequence alignment Neural Network neural networks (computer) NH interactions protein protein databases proteins secondary protein structure sequence alignment sequence-to-structure network structure-to-structure network

BioMeTool Content

http://metals.zesoi.fer.hr [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features

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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TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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Calculation of protein isoelectric pointTool Content

http://isoelectric.ovh.org/ [open in a new window]

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Protein > Biochemical Features

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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tagsamino acids bisection C++ calculation of isoelectric point free program isoelectric point isoelectric point calculator pH pI pK protein

CAPS-DBDatabase Content

http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home [open in a new window]

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Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Databases

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.

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
CAPS-DB: a structural classification of helix-capping motifs.20120
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CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das [open in a new window]

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Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Integrating protein annotation resources through the Distributed Annotation System200523
NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

Cell++Tool Content

http://sourceforge.net/projects/cellpp/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

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.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
Cell++--simulating biochemical pathways200619
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tagsbiochemistry biological models cell physiological phenomena computer simulation programming languages proteome signal transduction
setsUniversity of Toronto

CharProtDBDatabase Content

http://www.jcvi.org/charprotdb/index.cgi/home [open in a new window]

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Literature > Databases
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Databases

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.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
CharProtDB: a database of experimentally characterized protein annotations20121
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CHpredictTool Content

http://www.imtech.res.in/raghava/chpredict [open in a new window]

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Protein > Biochemical Features
Protein > Networks & Interactions, Pathways and Enzymes

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.

This content is being maintained by raghavagps.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network20063
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tagsalgorithms alpha H O amino acid sequence ANN C alpha H pi computer simulation hydrogen bonding hydrogen bonding interactions molecular models molecular sequence data neural networks (computer) protein databases protein sequence analysis proteins secondary protein structure weak interactions

CUPSATTool Content

http://cupsat.uni-koeln.de/ [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Biochemical Features

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
NAR Web Server Issue 2006
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tagsmolecular structure point mutation protein databases protein denaturation protein engineering protein folding proteins secondary protein structure solvents

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth [open in a new window]

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Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

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

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins20112
NAR Web Server Issue 2011
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tagsamino acids binding sites ligands molecular models peptide hydrolases protein conformation proteins west nile virus

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/ [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

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.

links directory index: 89
TitlePublication YearGoogle Scholar Citation Count
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification200625
DiANNA: a web server for disulfide connectivity prediction200564
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.20050
NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

DISULFINDTool Content

http://disulfind.dsi.unifi.it/ [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

links directory index: 252
TitlePublication YearGoogle Scholar Citation Count
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence20111
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence200825
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server200689
Disulfide connectivity prediction using recursive neural networks and evolutionary information2004137
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

eBioinformaticsResource Content

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

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DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Identification, Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

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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EMBOSSTool Content

http://emboss.bioinformatics.nl/ [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
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Identification, Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

links directory index: 2541
TitlePublication YearGoogle Scholar Citation Count
EMBOSS: the European Molecular Biology Open Software Suite20002541
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external linksLink on Wikipedia
tagsmolecular biology sequence alignment

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