Morph2 Server

From Info

The server can be found here NOTE: For the time being, we are not archiving morphs for long-term storage. Please retrieve your morph result(s) within a few days of job submission. We apologize for any inconvenience this may cause.

Contents 1 Introduction to Morph2 2 Homogenization Methods 2.1 Homology modeling 2.2 Alignment homogenization 3 Sample input files 4 Contact

Introduction to Morph2

Morph2 is a morphing server, similar to the Morph Server, but specifically designed for morphing between similar 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 Morph2 database.

Homogenization Methods

Morph2 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. Morph2 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 Alanine or 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 Morph2, 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 Morph2, contact robert.bjornson@yale.edu