Hi. I would like to understand what is meant by energy minimization in case of protein models. I've recently started learning about homology modeling. Furthermore, I would like to know what tools can be used for such purposes. I know Chimera has this option, but i would like to know what's the purpose behind it. Thank you.
Energy minimization is essentially about "settling" the model into a relatively energetically favorable state. Protein structures (whether from crystallography, NMR, homology modelling, or docking) often have errors of various magnitude: atoms partially overlapping, sidechains in the wrong positions, etc. Energy minimization looks for the pathway that gives the most reduction in the overall energy of the system, relaxing bond lengths, angles, non-bonded interactions etc. into more favorable states. Note that it will only ever settle the structure into a local (not global) energy minimum, but it will usually at least give you a structure that will run in a dynamic simulation without crashing. It won't work miracles, though: major errors in your starting structure will usually lead to major errors in your "minimized" structure. Note that closely watching your minimization trajectory to see what moves the most can be a good way of identifying errors in your structure in the first place.
As to programs that can do minimization: any program that can do molecular dynamics will also have a minimization function. Try NAMD or GROMACS (both free) for example.
Energy minimization is essentially about "settling" the model into a relatively energetically favorable state. Protein structures (whether from crystallography, NMR, homology modelling, or docking) often have errors of various magnitude: atoms partially overlapping, sidechains in the wrong positions, etc. Energy minimization looks for the pathway that gives the most reduction in the overall energy of the system, relaxing bond lengths, angles, non-bonded interactions etc. into more favorable states. Note that it will only ever settle the structure into a local (not global) energy minimum, but it will usually at least give you a structure that will run in a dynamic simulation without crashing. It won't work miracles, though: major errors in your starting structure will usually lead to major errors in your "minimized" structure. Note that closely watching your minimization trajectory to see what moves the most can be a good way of identifying errors in your structure in the first place.
As to programs that can do minimization: any program that can do molecular dynamics will also have a minimization function. Try NAMD or GROMACS (both free) for example.
3drefine is online tool which will minimize the model structure online and i3Drefine is stndalone tool for linux.
The best explanation why EM needed is given in its FAQ just go through given link.
http://sysbio.rnet.missouri.edu/3Drefine/faq.html
Dr. Tristan explained EM (Energy minimization) very well.
Gromacs is best. But you want to see on GUI interface, try SwissPDB viewer (free http://spdbv.vital-it.ch/disclaim.html ) for EM of your protein model. You can install it on Linux, windows or Mc.
Load the structure and select all, then do CNRL N for one step EM. For 10 steps you have to do same 10 times.You got result files in temp directory (in software directory). You can plot and see energy declination graph.
SwissPDBviewer is good for beginners who wants to know what and how EM performs.
Thanks
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