Contents
Overview
GLYCAM-Web provides tools for modeling the 3D structures of molecules and complexes containing carbohydrates. Current capabilities include:
- Oligosaccharide conformation modeling
- Glycoprotein 3D structure modeling
- View structures online
- Download structure files
- Download other information and files relevant to molecular modeling
Oligosaccharide Conformation Modeling
There are currently five interfaces for modeling oligosaccharide conformations:
- The Carbohydrate Builder (point-and-click interface)
- The Oligosaccharide Libraries (pre-set primary sequences for common glycans)
- Text box for direct entry of a primary sequence
- URL directive for sending a primary sequence to the modeler
- The GAG Builder (point-and-click interface for constructing GAGs)
All five interfaces use same background build process. Having generated a model, you can:
- View a 3D representation of the model online
- Download a PDB-style file containing the model
- Download files for input to an AMBER simulation
- Download other files (see main Oligosaccharide Modeling documentation)
Glycoprotein 3D Structure Modeling
The Glycoprotein Builder allows you to generate 3D models of glycoproteins. First, upload a PDB file containing the protein and then attach glycans to relevant glycosylation sites. The glycans are generated using any of the Oligosaccharide Conformation Modeling interfaces except the GAG Builder.
After constructing the model, you can:
- View a 3D representation of the model online
- Download a PDB-style file containing the model
- Download files for input to an AMBER simulation
- Download other files (see main Oligosaccharide Modeling documentation)
PDB Preprocessing
As part of the Glycoprotein Builder, your PDB file will be pre-processed for use with many of the utilities in the AMBER simulation suite. However, there might be times when you only want a pre-processed PDB (without any glycans added). For this, you have two options. One, you can use the Glycoprotein Builder without adding any glycans. You will need to use this option if you want to add solvent or generate AMBER simulation input files. However, if you only want a pre-processed PDB, you can use our PDB Preprocessor. It uses the same mechanism as the Glycoprotein Builder. The only difference is the simpler interface.
Other Data and Downloads
Force Field Parameters
All current and previous GLYCAM force field parameters are available for download at the parameters page.
Software
Most of the back-end software that we generate is open source and freely available to the public. The website interface itself isn’t, at this time, available, but almost everything else is.
GMML
The main software engine that powers GLYCAM-Web is the GLYCAM Molecular Modeling Library (GMML).
GEMS
GEMS, the GLYCAM Extensible Modeling Script, is a python interface to GMML. Gems is also used by the website.
GLYLIB
GLYLIB, the GLYCAM Programmers Libraries, is a sort-of precursor to GMML. Some of the other software available here relies on it.
Other Software for Download
Some other programs are also available, for example, released in association with a publication. Please see our Software page for more information.
Documentation
This page is part of the GLYCAM-Web documentation. Click here to access the main documentation page.