>
Tag
> Links tagged with 'molecular conformation'

Links tagged with 'molecular conformation'

RSS FeedCompact ViewList as XMLList as JSON

Found 17 links

Displaying 15 links

AD-ENMTool Content

http://enm.lobos.nih.gov

Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Molecular Dynamics and Docking

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsactins adenosine triphosphate animals binding sites biophysical phenomena biophysics dictyostelium dna polymerase beta dna-directed rna polymerases elasticity humans kinesin ligands mice molecular conformation molecular models molecular motor proteins myosins nucleotides principal component analysis protein binding protein conformation proton-translocating atpases protozoan proteins secondary protein structure statistical models structure-activity relationship taq polymerase tertiary protein structure theoretical models thermodynamics viral proteins x-ray crystallography

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click

Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms molecular conformation molecular models nucleic acid conformation protein conformation rna

ComSinDatabase Content

http://antares.protres.ru/comsin/.

Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

NAR Database Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

Frog2Tool Content

http://bioserv.rpbs.univ-paris-diderot.fr/Frog2

Other Molecules > Compounds
Other Molecules > Small Molecules

Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmolecular conformation molecular models pharmaceutical preparations stereoisomerism

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

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
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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

NQ-FlipperTool Content

https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php

Protein > 3-D Structure Prediction

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamides asparagine computational biology crystallography escherichia coli glutamine molecular conformation molecular models protein conformation protein databases protein folding proteins reproducibility of results statistical data interpretation stereoisomerism structural models thermodynamics

PDB2PQR ServerTool Content

http://pdb2pqr.sourceforge.net/

Protein > 3-D Structural Features
Protein > Biochemical Features

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.

NAR Web Server Issue 2004NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

PFPTool Content

http://pfp.technion.ac.il/

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

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PI2PETool Content

http://pipe.scs.fsu.edu/

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

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

PICTool Content

http://crick.mbu.iisc.ernet.in/~PIC/

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

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acids animals computational biology humans hydrogen bonding molecular conformation molecular models molecular structure plant proteins protein databases proteins

PINTSTool Content

http://www.russell.embl.de/pints/

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

Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals binding sites factual databases humans molecular conformation molecular models protein conformation protein databases protein folding protein structural homology proteins quaternary protein structure sequence alignment sequence analysis tertiary protein structure

ProSA-webTool Content

https://prosa.services.came.sbg.ac.at/prosa.php

Protein > 3-D Structure Prediction

ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology escherichia coli molecular conformation molecular models protein conformation protein databases protein denaturation protein folding proteins sequence analysis

RCITool Content

http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py

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

RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals biomolecular nuclear magnetic resonance carbon isotopes computational biology computer simulation humans hydrogen magnetic resonance spectroscopy molecular conformation nitrogen isotopes pliability protein conformation proteins reproducibility of results statistical models