Sculpting protein conformations: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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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.
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-This page is under development starting February 29, 2020. Please come back later to see it more fully developed.
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-Planned contents include PyMOL, Samson, and (now defunct) Sculpt. These programs enable protein conformations to be "sculpted" by dragging with the mouse.
+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].
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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. 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.
 ==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]).
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 * Anchor points can be set that remain fixed during sculpting.
 * 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.
 '''Cons'''
-* Atomic clashes and unrealistic bond distances and angles may occur.
+* 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>
-* Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /><ref name="low-energy-paths" />.
+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.
-| width="400" |<qt>file=1al1-sculpting-samson-v4-400px.mp4|width=400|height=198|autoplay=false|controller=true|loop=false</qt>
-Sculpting [[1al1|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. [https://s3.us-east-2.amazonaws.com/molviz.org/downloads/Samson/1al1-sculpting-samson-v4.mp4 Higher resolution version].
 |}
 ==PyMOL==
+[[PyMOL]], originally developed by [[User:Warren DeLano|Warren DeLano]], is now maintained and licensed by [http://schroedinger.com Schr&ouml;dinger]. 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<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==
-* ''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., is described with the theoretical structure [[1ssr]].
+* [[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/Molecular modeling tools]]
 *[[Molecular modeling and visualization software]]
+* See the list of links above under PyMOL.
 ==References==
 <references />