· Plotting melting temperature
Synopsis: Matlab script to fit the CD data to compute the melting temperature. Important thing to remember is to arrange the data as in the attached example. The first row across is the temperature at which the CD spectrum was collected. Each column is the CD value at 250 - 200 nm in decrements of 0.1 nm. If your data are arranged differently, then you would need to go in and modify the script a little. This shouldn't be too difficult. Here're the script and an example file.
The temperature fit is done as in John and Weeks, Protein Science 9, 1416 (2000). To be able to implement the two parameter fit in Matlab without using any extra module, I simply alternate between Tm and deltaH fits until both values converge.
data.xlsx, plot tm.m
Note: Admittedly, the input handling is a little kludgy but it gets the job done.
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· Identifying buried water molecules in a PDB structure
Synopsis: If a PDB file contains water molecules and you want to remove all water molecules except the buried water molecules, i.e. zero solvent accessible surface area (SASA).
Usage: source burwat.job data.lis
Note: You need to download naccess (http://www.bioinf.manchester.ac.uk/naccess/), which is the program I use to compute SASA. Here is 1x9q.pdb used in the example.
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· Symmetry application of a mutation in one subunit to all other subunits in a homooligomer
Synopsis: The file symmut.tcl allows you to introduce a mutation in one subunit of a homooligomer, and propagate the same mutation to other subunits
Example: In a tetramer containing subunits A/B/C/D, introduce a mutation in A. Then apply "symmut1 A B", "symmut1 A C", and "symmut1 A D" to write symmut_B.pdb, symmut_C.pdb and symmut_D.pdb. The new file can be combined to generate a mutant tetramer containing an identical mutation.
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· Residue specific rmsd calculation
res_rmsd.tcl
Synopsis: Run through the entire MD trajectory to compute the residue specific rmsd (for backbone atoms only).
Note: First, apply translation and rotation to remove macroscopic displacement by applying "super", which superimposes all subsequent frames to the first frame
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· Computing the buried surface area for a trajectory
Synopsis: A simple script to compute the buried surface area of a protein complex A/B for each frame in an MD trajectory (bursurf.tcl)
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· Many other useful scripts can be downloaded from the vmd and namd websites.
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· For entropy calculation from MD trajectories, carma provides both Schlitter and Andricioaei estimates. To compute the entropy change during a binding event, you repeat the simulation for the apo and complex structures and substract the entropy of the complex from the entropy of the starting structures.
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· For solvation calculation, one can use the adaptive PB solver (APBS) developed by Baker et al.
For example, in order t to compute the solvation energy for a trajectory,
1. create PDB files corresponding to simulated structures (getpdb.tcl).
2. generate pqr files for each snapshot (pqr.sh) using standalone pdb2pqr.
3. compute the solvation energy using APBS (apbs.sh)
4. extract the solvation energy from the corresponding log files (epb.sh)
The solvation energy Epb is then added to the electrostatic energy computed in a homogeneous medium in order to calculate the free energy of interaction.
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