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Proteinstein: A Server for peptide construction

PDB linker Database

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Proteinstein: A Server for peptide construction | proteinstein.com Reviews
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Proteinstein: A Server for peptide construction | proteinstein.com Reviews

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PDB linker Database

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Proteinstein: A Server for peptide construction

http://www.proteinstein.com/thanks.html

Protein linking by fragments found in nature. Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, Journal of Computational Chemistry, 25: 1400-1415, 2004.

2

Proteinstein: A Server for peptide construction

http://www.proteinstein.com/FAQ.html

Protein linking by fragments found in nature. So far nobody has asked any questions. When they are asked you should be able to find them, along with answers, here.

3

Proteinstein: A Server for peptide construction

http://www.proteinstein.com/about.html

Protein linking by fragments found in nature. Proteinstein was created to address a need encountered in our lab of designing small proteins based on known structures. We had a framework and knowledge of its geometry, but required linkers to connect the pieces of the framework. After writing the software to perform this task we decided to make the server publicly available for other researchers to use. Here the server takes the blue fragments and joins them together with the red linker. Written and mainta...

4

Proteinstein: A Server for peptide construction

http://www.proteinstein.com/help.html

Protein linking by fragments found in nature. This help describes each input field in the order they appear on the main page. Expected input is a PDB file. Only the "ATOM" entries are required) containing two fragments. These can be made several ways. The easiest way to experiment with this is to download a pdb file from the Protein Data Bank. And delete a set of residues, leaving only a couple fragments of the original protein. Another method is to get two fragments and use a program like VMD. However m...

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Proteinstein: A Server for peptide construction

Protein linking by fragments found in nature. Upload a PDB file with the fragments to be joined. PDB file containing fragments to be joined. The results are sent to this address). C terminus of the first fragment, N terminus of the second. How many residues you want joining the two fragments. Number of models to generate. Max error in distance:. Max error in angles:.

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