> 1. Try our coiled-coil modelling server > https://pharm.kuleuven.be/apps/biocryst/ccfold.php
Some more explanation here. This server runs our CCFold algorithm (Guzenko & Strelkov (2017) Bioinformatics, article btx551). CCFold is a threading-type algorithm which was specifically designed to model coiled coils from amino-acid sequence. This is why it is fundamentally faster than generic algorithms like Quark or Rosetta. CCFold is also trivial to run using our web server or a local installation if you prefer. The modelling accuracy of CCFold was discussed in the Guzenko and Strelkov paper cited above. Sergei ________________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Sergei Strelkov <[email protected]> Sent: Tuesday, October 8, 2019 14:14 To: [email protected] Subject: Re: [ccp4bb] coiled coil molecular replacement Dear Tommi, With coiled coils you certainly want to use the best search model possible. Coiled coils are elongated structures and a small local inaccuracy of your search model may result in large differences (in terms of overall rmsd) with respect to the true structure. Two suggestions: 1. Try our coiled-coil modelling server https://pharm.kuleuven.be/apps/biocryst/ccfold.php 2. Prepare a set of partial models (corresponding to various parts/lengths e.g. 50-60% of the total length) and attempt MR with each of them. In our experience the standard algorithms (MolRep/Phaser) can also work well. It depends a lot on the space group and particular packing of your dimers (dense packings being the most challenging). Hope this helps, Sergei Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of Pharmaceutical Sciences, KU Leuven O&N2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography ________________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Kajander, Tommi A <[email protected]> Sent: Monday, October 7, 2019 23:33 To: [email protected] Subject: [ccp4bb] coiled coil molecular replacement Hello, We have a bit tricky case of coiled coil protein with good data (2.05Å) for dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way to solve such cases, if you know other good programs please suggest (Better yet if there is a clear how-to manual) Some technical tips on usage for generation of fragments for AMPLE would be of help, not completely on top of that… (running the QUARK server, the real sequence is bit over 200 aa so not sure what is the best approach here? Rosetta? any how-to for that.. well i am running Robetta fragments too). with AMPLE can I do this with the online server or better run locally (need Rosetta installed I take it?) Suppose I could try Rosetta-MR also, but to my recollection that requires some kind of a phaser hit first to be improved, and i dont think I am there. Thanks for any comments, Best, Tommi ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
