Sculpting protein conformations: Difference between revisions
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A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | ||
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|'''Pros''' | |||
* Atomic clashes are avoided. | * Atomic clashes are avoided. | ||
* Minimization occurs in real time during dragging. | * Minimization occurs in real time during dragging. | ||
'''Cons''' | |||
* PyMOL is not free, although many institutions have site licenses, and you may be able to obtain a free version for educational uses. | * PyMOL is not free, although many institutions have site licenses, and you may be able to obtain a free version for educational uses. | ||
| width="600" |<qt>file=1al1-stretch-pymol.mp4|width=615|height=260|autoplay=false|controller=true|loop=false</qt> | |||
Sculpting [[1al1|1AL1]] with PyMOL (screen capture}. A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
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==Sculpt (defunct)== | ==Sculpt (defunct)== | ||
Revision as of 22:54, 4 March 2020
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This page is under development starting February 29, 2020. Please come back later to see it more fully developed. |
Planned contents include PyMOL, Samson, and (now defunct) Sculpt. These programs enable protein conformations to be "sculpted" by dragging with the mouse.
Sometimes it is instructive to change the conformation of a protein model. Typically this means "sculpting" an experimentally-determined (empirical) model into a hypothetical conformation with some functional significance[1]. Here are described software packages that enable this to be done manually, using the mouse to drag portions of the original model into desired conformations.
As you sculpt a protein model, you are morphing it into a new conformation. However, molecular morphing usually means saving a movie or animation that shows interpolated transitioning between two earlier-saved conformations, which may be empirical or theoretical. There are many examples of molecular morphs in Proteopedia. Slides explaining how to morph a sculpted protein are available at tinyurl.com/sculpting-proteins.
SamsonSamson
The free, open-source program Samson is available from samson-connect.net and in February 2020 is under active development by OneAngstrom.Com: see What's New in Samson 2020?. Samson has an extension application named Twister that enables dragging portions of a protein into new conformations with the mouse. Real-time minimization occurs while dragging, following the as-rigid-as-possible interpolation path[2][3]. You can click on atoms to set anchor points (shown as gold balls) that remain fixed during dragging. A video showing how to do this, step by step, is available at tinyurl.com/sculpting-proteins.
Twister alone does not prevent atomic clashes. To do that, add hydrogens (click +H in the Quick Access bar) and turn on Minimize (in the Home tab), which applies a universal force field. After changing the conformation, turn off Twister (press Esc) to release the anchor points, and atom positions will be adjusted automatically to remove any clashes.
Pros
Cons
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Sculpting 1AL1 with Samson (screen capture}. An anchor point (gold ball) was set at left before the movie starts. Mid-way, an anchor point was set in the middle of the polypeptide. Higher resolution version. Minimize was not turned on in this movie. |
PyMOLPyMOL
PyMOL, originally developed by Warren DeLano, is now maintained and licensed by Schrödinger. It includes a sculpting mode. A video showing how to do this, step by step, is available at tinyurl.com/sculpting-proteins.
Pros
Cons
|
Sculpting 1AL1 with PyMOL (screen capture}. A video showing how to do this, step by step, is available at tinyurl.com/sculpting-proteins. |
Sculpt (defunct)Sculpt (defunct)
Related ResourcesRelated Resources
- Sculpt[4], a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr., is described with the theoretical structure 1ssr.
- User:Wayne Decatur/Generate Unfolded Structures
- User:Wayne Decatur/Molecular modeling tools
- Molecular modeling and visualization software
ReferencesReferences
- ↑ 1.0 1.1 Nguyen MK, Jaillet L, Redon S. ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths. J Comput Aided Mol Des. 2019 Aug;33(8):705-727. doi: 10.1007/s10822-019-00216-w. , Epub 2019 Aug 21. PMID:31435895 doi:http://dx.doi.org/10.1007/s10822-019-00216-w
- ↑ 2.0 2.1 Nguyen MK, Jaillet L, Redon S. As-Rigid-As-Possible molecular interpolation paths. J Comput Aided Mol Des. 2017 Apr;31(4):403-417. doi: 10.1007/s10822-017-0012-y., Epub 2017 Mar 20. PMID:28321532 doi:http://dx.doi.org/10.1007/s10822-017-0012-y
- ↑ 3.0 3.1 Nguyen MK, Jaillet L, Redon S. Generating conformational transition paths with low potential-energy barriers for proteins. J Comput Aided Mol Des. 2018 Aug;32(8):853-867. doi: 10.1007/s10822-018-0137-7., Epub 2018 Aug 1. PMID:30069648 doi:http://dx.doi.org/10.1007/s10822-018-0137-7
- ↑ Surles MC, Richardson JS, Richardson DC, Brooks FP Jr. Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system. Protein Sci. 1994 Feb;3(2):198-210. PMID:8003957