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Links tagged with 'molecular structure'

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Found 33 links

Displaying 15 links

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

NAR Web Server Issue 2007
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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

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

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

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

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

NAR Web Server Issue 2005
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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

DSHIFTTool Content

http://www.chem.cuhk.edu.hk/DSHIFT/

DNA > Structure and Sequence Feature Detection

DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

NAR Web Server Issue 2007
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tagsalgorithms base sequence biomolecular nuclear magnetic resonance carbon computational biology computer simulation dna magnetic resonance spectroscopy molecular models molecular sequence data molecular structure nucleic acid conformation oligonucleotides phosphorus programming languages protons reproducibility of results sensitivity and specificity stochastic processes temperature

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

ESPriptTool Content

http://espript.ibcp.fr/ESPript/ESPript/index.php

Sequence Comparison > Alignment Editing and Visualization

Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology dna-binding proteins molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

FF - Fragment FinderTool Content

http://cluster.physics.iisc.ernet.in/ff/

Protein > 3-D Structural Features
Protein > Domains and Motifs

FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.

NAR Web Server Issue 2005
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tagsamino acid motifs molecular structure proteins

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

NAR Web Server Issue 2005
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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

FrogTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog

Other Molecules > Small Molecules

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).

NAR Web Server Issue 2007
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tagsalgorithms chemical models chemistry computational biology computer simulation ligands molecular conformation molecular structure pharmaceutical chemistry pliability protein databases proteins quantitative structure-activity relationship x-ray crystallography

GlyNest and CASPERTool Content

http://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation

Other Molecules > Carbohydrates

GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.

This content is being maintained by luetteke.

NAR Web Server Issue 2006
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tagsalgorithms automatic data processing bacterial capsules bacterial polysaccharides biomolecular nuclear magnetic resonance carbohydrate conformation carbohydrate sequence carbohydrates carbon isotopes computational biology computer simulation factual databases forecasting glycopeptides glycoproteins hydrogen magnetic resonance spectroscopy molecular models molecular sequence data molecular structure o antigens oligosaccharides polysaccharides systems integration three-dimensional imaging

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

NAR Web Server Issue 2005
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tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

NAR Web Server Issue 2007
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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

MolProbityTool Content

http://molprobity.biochem.duke.edu/

Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

NAR Web Server Issue 2004NAR Web Server Issue 2007
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tagscomputational biology hydrogen bonding hydrogens molecular graphics molecular models molecular structure nucleic acid conformation protein protein conformation reproducibility of results rna structure validation three-dimensional imaging