> > 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 43 links

Displaying 15 links

AnalyCysDatabase Content

http://bioinformatics.univ-reunion.fr/analycys/

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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CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

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.

NAR Web Server Issue 2005
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tagsprotein sequence analysis systems integration

CUPSATTool Content

http://cupsat.uni-koeln.de/

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.

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

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.

NAR Web Server Issue 2011
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DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/

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.

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/

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.

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/

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 > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

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/

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 > 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

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

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tagsmolecular biology sequence alignment

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

NAR Web Server Issue 2004
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

H++Tool Content

http://biophysics.cs.vt.edu/H++

Protein > 3-D Structural Features
Protein > Biochemical Features

H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.

This content is being maintained by onufriev.

NAR Web Server Issue 2005
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tagsAMBER hydrogen hydrogen-ion concentration molecular dynamics Molecular modeling pK protonation

HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

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.

This content is being maintained by flebeda.

NAR Web Server Issue 2009
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

MASCOT (Matrix Science)Tool Content

http://www.matrixscience.com/

Protein > Biochemical Features
Protein > Proteomics

Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.

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tagsamino acid sequence amino acids factual databases mass spectrometry molecular sequence data molecular weight nucleic acids probability protein biosynthesis proteins

MODiTool Content

http://prix.uos.ac.kr/research.jsp

Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

NAR Web Server Issue 2006
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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

Tags associated with subcategory 'Protein/Biochemical Features'

proteins protein conformation protein databases protein sequence analysis computational biology molecular sequence data amino acid sequence molecular models algorithms sequence alignment animals static electricity computer simulation secondary protein structure neoplasms hydrogen hydrogen bonding mathematical computing ligands isoelectric point protein structural homology neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis proprotein convertases molecular conformation molecular structure software design systems integration transcription factors anti-infective agents single nucleotide polymorphism sensitivity and specificity programming languages solvents acyltransferases reproducibility of results rats multigene family archaeal genes viral matrix proteins muramidase automatic data processing genetic polymorphism quantitative structure-activity relationship x-ray crystallography ovomucin plant lectins plant proteins recombinant proteins quaternary protein structure ribosomal proteins saccharomyces cerevisiae proteins gene expression profiling genes genetic promoter regions mice female equipment failure analysis sequence tagged sites biomedical technology assessment breast neoplasms drosophila melanogaster caenorhabditis elegans archaeal genome antimicrobial cationic peptides molecular evolution neural networks (computer) protein binding cell membrane ubiquitin sequence analysis structure-activity relationship dna sequence analysis open reading frames rna sequence analysis proteome beta-lactamases catalytic domain nucleic acids probability protein biosynthesis disulfide bridges post-translational protein processing peptides factual databases mass spectrometry molecular weight histidine humans protein interaction mapping lipids dna eukaryotic cells evaluation studies as topic bacterial genome conserved sequence hormones automated pattern recognition bacterial genes base sequence