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Links tagged with 'hydrogen'

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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.

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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

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.

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

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
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tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

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