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Links tagged with 'macromolecular substances'

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Found 23 links

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BIND - The Biomolecular Interaction Network DatabaseDatabase Content

http://bond.unleashedinformatics.com/Action

Protein > Interactions, Pathways, Enzymes

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

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tagsamino acid sequence animals dna factual databases humans macromolecular substances molecular biology protein databases protein interaction mapping proteins rna sequence alignment statistical models tertiary protein structure

BIND SOAPTool Content

http://soap.bind.ca/

Computer Related > Web Services

BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API).

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tagsamino acid sequence animals macromolecular substances protein databases protein interaction mapping proteins sequence alignment tertiary protein structure

BIOBASE Gene Regulation databasesDatabase Content

http://www.gene-regulation.com/pub/databases.html

Protein > Interactions, Pathways, Enzymes

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

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tagsanimals binding sites chromatin chromosomes database management systems developmental gene expression regulation dna-binding proteins eukaryotic cells forecasting gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans macromolecular substances mice nuclear matrix nuclear proteins nucleic acid databases oligonucleotide array sequence analysis protein databases saccharomyces signal transduction systems integration tissue distribution transcription factors

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

NAR Web Server Issue 2004
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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

BioPythonTool Content

http://biopython.org/

Computer Related > Bio-* Programming Tools

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

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tagscomputational biology computer simulation computer systems database management systems humans macromolecular substances molecular models programming languages protein conformation protein databases
setsOpen Bioinformatics Foundation

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

DIPDatabase Content

http://dip.doe-mbi.ucla.edu/

Protein > Interactions, Pathways, Enzymes

The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.

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tagsanimals bacterial proteins computational biology factual databases forecasting fungal proteins helicobacter pylori humans information services macromolecular substances molecular models precipitin tests protein binding protein databases proteins reproducibility of results tertiary protein structure two-hybrid system techniques

EMDataBank.orgDatabase Content

http://EMDataBank.org

Other Molecules > Databases
Protein > Databases

EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes.

NAR Database Issue 2011
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tagscryoelectron microscopy factual databases macromolecular substances molecular models protein databases proteins

GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

NAR Web Server Issue 2006
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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/

Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

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tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

I2I-SiteEngineTool Content

http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

NAR Web Server Issue 2005
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tagsalgorithms amino acids binding sites computational biology ligands macromolecular substances multiprotein complexes protein conformation protein interaction mapping proteins secondary protein structure

MolSurferTool Content

http://projects.villa-bosch.de/dbase/molsurfer/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

NAR Web Server Issue 2003
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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

MONSTERTool Content

http://monster.northwestern.edu/

Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.

This content is being maintained by samseaver.

NAR Web Server Issue 2004
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tagsmacromolecular substances molecular structure nucleic acids peptides proteins

NOMAD-RefTool Content

http://lorentz.immstr.pasteur.fr/nomad-ref.php

Protein > Molecular Dynamics and Docking

Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.

NAR Web Server Issue 2006
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tagscarrier proteins computer simulation dna dna-binding proteins dna-directed dna polymerase dna-directed rna polymerases escherichia coli proteins ligands macromolecular substances mathematical computing molecular models molecular structure motion neural networks (computer) protein conformation proteins x-ray diffraction

PatchDockTool Content

http://bioinfo3d.cs.tau.ac.il/PatchDock/

Protein > Molecular Dynamics and Docking

PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

NAR Web Server Issue 2005
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tagsalgorithms alpha-amylases antibodies antigen receptors bacterial proteins binding sites capsid proteins computational biology exotoxins influenza virus hemagglutinin glycoproteins ligands macromolecular substances membrane proteins molecular models multiprotein complexes phosphoenolpyruvate sugar phosphotransferase system protein conformation protein interaction mapping protein-serine-threonine kinases proteins secondary protein structure viral antigens