Sculpting protein conformations: Difference between revisions
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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<ref name="transition-paths">PMID:31435895</ref>. 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 in real time. However, [[Morphs|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 [[Morphs|many examples of molecular morphs]] in Proteopedia. Slides explaining how to morph a sculpted protein are available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
==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]: see [https://documentation.samson-connect.net/whats-new-in-samson-2020-the-open-molecular-modeling-platform/ 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<ref name="arap1">PMID:28321532</ref><ref name="low-energy-paths">PMID: 30069648</ref>. | The free, open-source program Samson is available from [http://samson-connect.net samson-connect.net] and in February 2020 is under active development by [http://oneangstrom.com OneAngstrom.Com]: see [https://documentation.samson-connect.net/whats-new-in-samson-2020-the-open-molecular-modeling-platform/ 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<ref name="arap1">PMID:28321532</ref><ref name="low-energy-paths">PMID: 30069648</ref>. 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 [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | ||
Twister alone does not prevent atomic clashes, but they can be avoided by turning on '''''Minimize''''', which applies a ''universal force field''. This is demonstrated in the movie available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. Samson can also create simulations that use any of a number of force fields provided, such as GROMACS (not illustrated here -- see [https://documentation.samson-connect.net/simulating-small-molecules-graphene-and-proteins/ Simulating small molecules and proteins]). | |||
{| class="wikitable" | {| class="wikitable" | ||
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* Anchor points can be set that remain fixed during sculpting. | * Anchor points can be set that remain fixed during sculpting. | ||
* Minimization occurs in real time during dragging. | * Minimization occurs in real time during dragging. | ||
* Activating ''Minimize'' avoids clashes and maintains correct geometry. | |||
* Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /><ref name="low-energy-paths" />. | |||
* Free software. | * Free software. | ||
'''Cons''' | '''Cons''' | ||
* No official documentation for using ''Twister'' from the ''Samson'' team in March, 2020, but see the step by step video at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
* No official documentation for using ''Twister'' from the ''Samson'' team. | | width="600" |<qt>file=1al1-sculpting-samson-v5-600px.mp4|width=600|height=307|autoplay=false|controller=true|loop=false</qt> | ||
Sculpting [[1al1|1AL1]] with Twister in 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. [https://s3.us-east-2.amazonaws.com/molviz.org/downloads/Samson/1al1-sculpting-samson-v5.mp4 Higher resolution version]. ''Minimize'' was not turned on in this movie. | |||
|<qt>file=1al1-sculpting-samson- | |} | ||
==PyMOL== | |||
[[PyMOL]], originally developed by [[User:Warren DeLano|Warren DeLano]], is now maintained and licensed by [http://schroedinger.com Schrödinger]. It includes a sculpting mode. | |||
A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
{| class="wikitable" | |||
|- | |||
|'''Pros''' | |||
* Atomic clashes are avoided. | |||
* Minimization occurs in real time during dragging. | |||
'''Cons''' | |||
* Sculpting in PyMOL is described as unsupported (see below) and there is no detailed documentation. However see the step-by-step instructional movie at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
* 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]. | |||
|} | |} | ||
= | * [https://www.youtube.com/watch?v=d5SP28Gt-7Y Using PyMOL sculpting to tighten/untie a trefoil knot] is a useful video on YouTube. | ||
* [https://pymolwiki.org/index.php/Molecular_Sculpting Molecular Sculpting] in the PyMOL wiki, a brief set of instructions written by [[User:Warren DeLano|Warren DeLano]]. | |||
* [https://pymol.org/dokuwiki/doku.php?id=sculpting sculpting] at pymol.org lists a few commands. | |||
*[https://pymol.org/dokuwiki/doku.php?id=setting:sculpt setting:sculpt] at pymol.org lists many commands. | |||
*[https://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures] at pymolwiki.org explains command-based methods for sculpting in PyMOL. | |||
==Sculpt (defunct)== | ==Sculpt (defunct)== | ||
Sculpt<ref name="sculpt" /> is no longer available. It was initially released in 1994 by Mark Surles, [[User:Jane S. Richardson|Jane Richardson]], David Richardson, and Frederick P. Brooks, Jr., and is described with the theoretical structure [[1ssr]]. Formerly it was available as a stand-alone program, and also it was built-into [[Chime]]. A simulation of inhibitor binding to HIV protease that was created with Sculpt can be viewed at [[Molecular Playground/HIV Protease Inhibitor]]. A simulation of water molecules coalescing into a nano-droplet was done with Sculpt, and can be found at [http://molviz.org MolviZ.Org] or by going directly to [http://biomodel.uah.es/en/water/p2.htm Water at BioModel]. | |||
==Related Resources== | ==Related Resources== | ||
* ''Sculpt''<ref name="sculpt">PMID:8003957</ref>, a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr. | * [[1ssr|1SSR]], a theoretical structure, is accompanied by a publication describing ''Sculpt''<ref name="sculpt">PMID:8003957</ref>, a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr.. | ||
*[[User:Wayne Decatur/Generate Unfolded Structures]] | *[[User:Wayne Decatur/Generate Unfolded Structures]] | ||
*[[User:Wayne Decatur/Molecular modeling tools]] | *[[User:Wayne Decatur/Molecular modeling tools]] | ||
*[[Molecular modeling and visualization software]] | *[[Molecular modeling and visualization software]] | ||
* See the list of links above under PyMOL. | |||
==References== | ==References== | ||
<references /> | <references /> | ||
Latest revision as of 20:14, 5 March 2020
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 in real time. 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, but they can be avoided by turning on Minimize, which applies a universal force field. This is demonstrated in the movie available at tinyurl.com/sculpting-proteins. Samson can also create simulations that use any of a number of force fields provided, such as GROMACS (not illustrated here -- see Simulating small molecules and proteins).
Pros
Cons
|
Sculpting 1AL1 with Twister in 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. |
- Using PyMOL sculpting to tighten/untie a trefoil knot is a useful video on YouTube.
- Molecular Sculpting in the PyMOL wiki, a brief set of instructions written by Warren DeLano.
- sculpting at pymol.org lists a few commands.
- setting:sculpt at pymol.org lists many commands.
- Modeling and Editing Structures at pymolwiki.org explains command-based methods for sculpting in PyMOL.
Sculpt (defunct)Sculpt (defunct)
Sculpt[4] is no longer available. It was initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr., and is described with the theoretical structure 1ssr. Formerly it was available as a stand-alone program, and also it was built-into Chime. A simulation of inhibitor binding to HIV protease that was created with Sculpt can be viewed at Molecular Playground/HIV Protease Inhibitor. A simulation of water molecules coalescing into a nano-droplet was done with Sculpt, and can be found at MolviZ.Org or by going directly to Water at BioModel.
Related ResourcesRelated Resources
- 1SSR, a theoretical structure, is accompanied by a publication describing Sculpt[4], a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr..
- User:Wayne Decatur/Generate Unfolded Structures
- User:Wayne Decatur/Molecular modeling tools
- Molecular modeling and visualization software
- See the list of links above under PyMOL.
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
- ↑ 4.0 4.1 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