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Links tagged with 'biomolecular nuclear magnetic resonance'

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Found 17 links

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CS23DTool Content

http://www.cs23d.ca

Protein > 3-D Structure Prediction

Chemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.

NAR Web Server Issue 2008
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tagsalgorithms biomolecular nuclear magnetic resonance protein conformation protein databases protein sequence analysis

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

DSSPcontTool Content

http://cubic.bioc.columbia.edu/services/DSSPcont/

Protein > 2-D Structure Prediction

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence biomolecular nuclear magnetic resonance hydrogen bonding molecular models proteins secondary protein structure

GeNMRTool Content

http://www.genmr.ca

Protein > 3-D Structure Prediction

Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.

NAR Web Server Issue 2009
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tagsalgorithms biomolecular nuclear magnetic resonance molecular models protein conformation protein databases reproducibility of results

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

HMDBDatabase Content

http://www.hmdb.ca/

Human Genome > Other Resources
Other Molecules > Metabolites

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical structure and relational query searches.

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tagsbiochemical phenomena biochemistry biomolecular nuclear magnetic resonance humans metabolism organ transplantation

MetaboAnalystTool Content

http://www.metaboanalyst.ca

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various univariate and multivariate statistical analysis for two/multi-group, one/two-factor, as well time-series data. For targeted metabolomic data, users can also perform functional enrichment analysis and pathway analysis.

This content is being maintained by Jeff Xia.

NAR Web Server Issue 2009
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tagsbiomolecular nuclear magnetic resonance cluster analysis mass spectrometry metabolomics

NMR Constraints AnalyserTool Content

http://molsim.sci.univr.it/constraint

Protein > 3-D Structure Prediction

NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.

NAR Web Server Issue 2010
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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation

PDBeDatabase Content

http://wwpdb.org

Protein > Databases

The Protein Data Bank in Europe (PDBe) manages the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank. PDBe has developed a browser to access and analyze the structural archive using classification systems. The PDBe web pages that describe individual PDB entries have plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. The SIFTS initiative provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases.

NAR Database Issue 2011
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tagsbiomolecular nuclear magnetic resonance europe protein conformation protein databases protein sequence analysis 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
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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

PREDITORTool Content

http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py

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

PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.

NAR Web Server Issue 2006
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tagsbiomolecular nuclear magnetic resonance molecular structure proteins torsion abnormality

PROSESS: A Protein Structure Evaluation Suite and ServerTool Content

http://www.prosess.ca

Protein > 3-D Structure Prediction

PROSESS (PROtein Structure Evaluation Suite and Server) is a comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.

NAR Web Server Issue 2010
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tagsbiomolecular nuclear magnetic resonance molecular models protein conformation x-ray crystallography

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
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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

RobettaTool Content

http://robetta.bakerlab.org/

Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.

NAR Web Server Issue 2004
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tagsalanine biomolecular nuclear magnetic resonance molecular models protein conformation protein sequence analysis protein structural homology proteins reproducibility of results tertiary protein structure

RosettaDesignTool Content

http://rosettadesign.med.unc.edu

Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography