Hello,
Recently I developed rigid body minimization algorithm and then extend it to also consider torsional flexibility. Here is the list of the papers:
Rigid Body Energy Minimization on Manifolds for Molecular Docking
http://pubs.acs.org/doi/abs/10.1021/ct300272j
A new Approach to Rigid Body Minimization with Application to Molecular Docking
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6426267
Flexible Refinement of Protein-Ligand Docking on Manifolds
http://www.nt.ntnu.no/users/skoge/prost/proceedings/cdc-2013/media/files...
As far as I know rigid body minimization and also flexible minimization(backbone, peptide, small molecule) are one of the main components of Rosetta protocol.
I was software engineer in Google and I am experienced programmer. I am interested to corporate these pieces and adopt them to the Rosetta environment or provide the source code to the Rosetta developers in case that they are interested to use it in the next generation of the code. I am not sure where I should start. It would be great if you let me know whether is this a reasonable and feasible direction.
Thanks
--Hanieh
Hi Hanieh,
It's great that you're interested in contributing your protocols to Rosetta! You're correct that flexible minimization is one of the important features of the Rosetta approach.
For various practical and logistical reasons, your best bet - as a published academic researcher - is probably to strike up a collaboration with one of the existing RosettaCommons labs. Perhaps some sort of research project where you seek to combine your algorithmic approach with some feature of Rosetta's, and evaluate how much of an improvement combining the two is.
If you go to https://www.rosettacommons.org/home, along the left hand side there's a list of the RosettaCommons member institutions, most of the time with links to the relevant PI's web pages. It'd also be worth while to look for research papers using Rosetta to do interesting things that might combine well with your algorithm, and then (after checking that they're a RosettaCommons-member lab) talk to the PI about striking up a collaboration. Once you're in a collaboration, the RosettaCommons PI will help you iron out the logistical issues with contributing your code to the Rosetta codebase.
Good Luck!
Great, Thanks!