[ccp4bb] mutation and minimization - SUMMARY
First off, thanks to all those who sent me their suggestions, a great variety indeed. Here's the summary: - turbo-frodo can do local rotamer optimization based on environment. - SCRWL and WHAT-IF are servers for homology modeling - Swiss PDB viewer/DeepView can also do homology modeling, but not natively on Linux - mutate and regularize geometry in coot - phenix.pdbtools from the command line (might be able to minimize only part of the model) Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] mutation and minimization
On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Chimera is pretty good for this. It has a Rotamer tool for making the substitution based on Dunbrack or Richardson libraries, and can screen based on probability / H-bonds formed / steric clashes: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html You can then use Chimera's Minimize Structure tool to minimize the side chain and/or the local environment or, if you're feeling frisky, the whole protein: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu Chimera home page: www.cgl.ucsf.edu/chimera
Re: [ccp4bb] mutation and minimization
On a similar extension to this topic, is there a good software out there for doing these kinds of modifications and minimizations for protein structures with chemicals entities (i.e., protein/inhibitor complexes). What I am looking to do is take a protein/inhbitor complex and add chemical modifications onto the inhibitor and see how they fit. so a little minimization/relaxation of the surrounding protein would be nice. It there a freely available software that will allow something like this, if not what commercial packages are cheapest/best at this? Thanks and sorry for hijacking this thread. -tom Tom J. Brett, PhD Assistant Professor of Medicine Division of Pulmonary and Critical Care Washington University School of Medicine Campus Box 8052, 660 S. Euclid Saint Louis, MO 63110 http://brettlab.dom.wustl.edu/ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Pettersen [p...@cgl.ucsf.edu] Sent: Friday, May 13, 2011 2:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] mutation and minimization On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Chimera is pretty good for this. It has a Rotamer tool for making the substitution based on Dunbrack or Richardson libraries, and can screen based on probability / H-bonds formed / steric clashes: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html You can then use Chimera's Minimize Structure tool to minimize the side chain and/or the local environment or, if you're feeling frisky, the whole protein: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu Chimera home page: www.cgl.ucsf.edu/chimerahttp://www.cgl.ucsf.edu/chimera
Re: [ccp4bb] mutation and minimization
On May 13, 2011, at 4:00 PM, Tom J. Brett wrote: On a similar extension to this topic, is there a good software out there for doing these kinds of modifications and minimizations for protein structures with chemicals entities (i.e., protein/inhibitor complexes). What I am looking to do is take a protein/inhbitor complex and add chemical modifications onto the inhibitor and see how they fit. so a little minimization/relaxation of the surrounding protein would be nice. It there a freely available software that will allow something like this, if not what commercial packages are cheapest/best at this? Thanks and sorry for hijacking this thread. Chimera also has a tool (Build Structure) that can be used for simple chemical modifications: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/editing/editing.html It's not as nice as some builders, but it can generally get the job done. Chimera can compute the charges on your modified structure by calling out to AmberTools/antechamber (included with the Chimera download) and then perform minimization. Charge computation might take awhile if the inhibitor is large-ish. This isn't to say that you shouldn't follow the protocol outlined by Saugata Hazra in another posting. It depends on your goals. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
[ccp4bb] mutation and minimization
Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] mutation and minimization
Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
Hi Andreas Without the x-ray data, phenix.pdbtools might do this (http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm) From the website: [phenix.pdbtools can] Perform model geometry regularization. Minimize geometry target to idealize bond lenghths, bond angles, planarities, chiralities, dihedrals, and non-bonded interactions. Try to specify to only optimize/minimize a selected part of the model (i.e. your point mutation and the residues around it). An alternative could be to re-refine the point-mutant model using the original x-ray data if you have access to it. Since you are making only a minor change it should work just fine (quickly and dirtily as asked for :)). hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-05-12 08:35, Andreas Förster wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas
Re: [ccp4bb] mutation and minimization
Or try SCWRL from Dunbrack's lab... --- On Thu, 5/12/11, gauri misra kamga...@gmail.com wrote: From: gauri misra kamga...@gmail.com Subject: Re: [ccp4bb] mutation and minimization To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, May 12, 2011, 12:52 PM You can try Swiss-PDB viewer.. 2011/5/12 Thomas Holder thomas.hol...@tuebingen.mpg.de Hi Andreas, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. PyMOL has a Mutagenesis wizard but you have to pick the best rotamer yourself. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Re: [ccp4bb] mutation and minimization
Hi If you are familiar with turbo-frodo, you can use it for mutagenesis and refinement . Just go inside the editing menu, replace the residue, save the file and REFINE the residue. You can also select the stretch of residues by picking the first and last residues so you will get the refinement (best rotamer) based on local environment. Amit Luthra, Ph.D. Post-Doctoral Fellow The Radolf Laboratory Department of Medicine University of Connecticut Health Center [w] http://spirocheteresearch.uchc.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andreas Förster [docandr...@gmail.com] Sent: Thursday, May 12, 2011 11:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] mutation and minimization Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
