Morph2 Server

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# The user supplies two proteins in the form of pdb files.
# The user supplies two proteins in the form of pdb files.
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# The two proteins are homogenized to have the same C-Alphas, using one of two methods (see below).
+
# The two proteins are homogenized to have the same amino acid residues, using one of two methods (see below).
-
# The second protein is superimposed on the first so as to minimize the RMSD between the C-Alphas.
+
# The second protein is superimposed on the first so as to minimize the RMSD between the alpha-carbon atoms.
# Each atom from the first protein is linearly interpolated toward its position in the second, using the desired number of steps. Optionally, after each step, the protein is minimized using gromacs in order to create more realistic intermediate positions.
# Each atom from the first protein is linearly interpolated toward its position in the second, using the desired number of steps. Optionally, after each step, the protein is minimized using gromacs in order to create more realistic intermediate positions.
# Finally all the steps are combined into an animation, and the results stored in the evolmorph database.
# Finally all the steps are combined into an animation, and the results stored in the evolmorph database.

Revision as of 11:06, 20 July 2008

Contents

Introduction to Evolmorph

Evolmorph is a morphing server, similar to the Morph Server, but specifically designed for morphing between evolutionarily related proteins rather than different conformations of the same protein.

The server can be found here.

Basically the steps are as follows:

  1. The user supplies two proteins in the form of pdb files.
  2. The two proteins are homogenized to have the same amino acid residues, using one of two methods (see below).
  3. The second protein is superimposed on the first so as to minimize the RMSD between the alpha-carbon atoms.
  4. Each atom from the first protein is linearly interpolated toward its position in the second, using the desired number of steps. Optionally, after each step, the protein is minimized using gromacs in order to create more realistic intermediate positions.
  5. Finally all the steps are combined into an animation, and the results stored in the evolmorph database.

Homogenization Methods

Evolmorph currently supports two methods of homogenizing the proteins so that they can be morphed:

Homology modeling

This method makes use of Modeller from the Sali lab. Modeller creates a new protein that has the sequence of the first, and the structure of the second. Evolmorph then morphs the original first protein against this new protein.

Alignment homogenization

This method was created by Amit Oberai (Yale Gerstein Lab). In this method, the two proteins are aligned by residue. Gaps are removed, and mismatches replaced by simple, common residues, usually Glycine. In this way, two new proteins are created that have (nearly) the structure of the originals, but with a common set of residues.

Sample input files

Here are some sample input files that you can use to test Evolmorph, organized by homology method.

Method
None 1u6r_0.pdb 1u6r_9.pdb
Homology 2bpf.pdb 2fmq.pdb
Alignment 1orq-pqs.pdb 1ors-pqs.pdb

Contact

For help with Evolmorph, contact robert.bjornson@yale.edu

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