Sculpting protein conformations: Difference between revisions
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==Samson== | ==Samson== | ||
The free, open-source program Samson is available from [http://samson-connect.net samson-connect.net] and in 2020 is under active development by [http://oneangstrom.com OneAngstrom.Com]. 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<ref name="arap1">PMID:28321532</ref>. | The free, open-source program Samson is available from [http://samson-connect.net samson-connect.net] and in 2020 is under active development by [http://oneangstrom.com OneAngstrom.Com]. 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<ref name="arap1">PMID:28321532</ref><ref name="low-energy-paths">PMID: 30069648</ref>. | ||
'''Pros''' | '''Pros''' | ||
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* Atomic clashes and unrealistic bond distances and angles may occur. | * Atomic clashes and unrealistic bond distances and angles may occur. | ||
* No official documentation for using ''Twister'' from the ''Samson'' team. | * No official documentation for using ''Twister'' from the ''Samson'' team. | ||
* Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /> | * Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /><ref name="low-energy-paths" />. | ||
==PyMOL== | ==PyMOL== | ||
Revision as of 21:55, 29 February 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.
SamsonSamson
The free, open-source program Samson is available from samson-connect.net and in 2020 is under active development by OneAngstrom.Com. 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].
Pros
- Anchor points can be set that remain fixed during sculpting.
- Minimization occurs in real time during dragging.
- Free software.
Cons
- Atomic clashes and unrealistic bond distances and angles may occur.
- No official documentation for using Twister from the Samson team.
- Interpolation methods are published[2][1][3].
PyMOLPyMOL
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