Justin, Single mutation for four residue. The number of mutants is 4x19=76 Of course , that is a tiny peptide library.
Best Shiyong On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul <[email protected]> wrote: > > > On 10/9/12 8:43 PM, Liu Shiyong wrote: >> >> Hi, >> >> Your expectation from MD is too much than reality. >> >> Peptide design is an open problem. Lots of elegant protocols are >> available. However, to my understanding, the core problem is still >> about protein-peptide docking and scoring. MD simulation only helps on >> some special cases. It is impossible that MD simulation is used to for >> screening peptide library. >> > > I would hardly call 4 different mutants a library. Plenty of methods exist > to enhance the sampling of such systems and have been used to great effect. > Computationally expensive to pull off properly? Yes. Impossible? In this > case, I would say no. > > -Justin > > >> >> On Thu, Oct 4, 2012 at 9:16 PM, rama david <[email protected]> >> wrote: >>> >>> Thank you for reply, >>> I read the recently published article in Biochemistry. >>> They worked on the same receptor that I am working. >>> ( as I mention in my previous mail) >>> They used NAMD software and I am using gromacs. >>> They sliced the receptor binding site and used the the solid support >>> to the binding site and did simulation. >>> So if I freeze the group is it will ok ?? >>> Is it possible in gromacs to fix the residue on solid immobilized >>> surface. >>> If it is how to do it?? >>> >>> my question is How to decide which group are remove and which group >>> should >>> keep in simulation.???? >>> >>> thank you in advance >>> Thank you for giving your valuable time and advice to me. >>> >>> With best wishes and regards, >>> Rama david >>> >>> >>> >>> >>> >>> >>> On Thu, Oct 4, 2012 at 6:11 PM, Thomas Evangelidis >>> <[email protected]>wrote: >>> >>>> I don't think AutoDock and Vina are suitable for peptide docking. I >>>> would >>>> first try the FlexPepDocking module of Rosetta which does ab initio >>>> folding >>>> of the peptide on the receptor, while moving the side-chains of the >>>> protein >>>> but leaves its backbone intact. Rosetta implements a knowledge-based >>>> scoring, which has been specifically designed for this task and is as >>>> fast >>>> as Vina or AutoDock. >>>> >>>> I would first do that and if I wouldn't get any reasonable results then >>>> I >>>> would move to MD starting from the top scored protein-peptide complexes >>>> created by Rosetta. >>>> >>>> Thomas >>>> >>>> >>>> On 4 October 2012 15:08, rama david <[email protected]> wrote: >>>> >>>>> Hi francesco, >>>>> >>>>> Thank you For reply. >>>>> I did docking but the result are not so impressive. >>>>> I used vina and autodock. >>>>> I also did virtual screening in autodock but the result are not upto >>>>> the >>>>> mark. >>>>> >>>>> Is the freezing of group can affect my system?? How much efficiency I >>>>> get >>>>> by these work?? >>>>> As these group are going to freeze in four simulation so if it affect >>>>> one >>>>> ligand it affect other >>>>> ligand also. >>>>> >>>>> I read article that did the work like me , >>>>> they sliced the binding residues and used the inert solid sphere to >>>>> support binding residues >>>>> instead of the freezing group other group. >>>>> >>>>> I think both way should have same effect..Am I right or wrong?? >>>>> >>>>> If you have any other way please suggest it.. >>>>> >>>>> With best wishes and regards >>>>> Rama david >>>>> >>>>> >>>>> On Thu, Oct 4, 2012 at 5:07 PM, francesco oteri >>>>> <[email protected]>wrote: >>>>> >>>>>> Hi, >>>>>> as far as I know, freezing just set velocities to 0 so you gain >>>>>> nothing >>>>>> freezing atoms. >>>>>> >>>>>> By the way, have you tried docking? It takes into account multiple >>>>>> conformation and >>>>>> orientation of the peptide and, depending upon the implemented >>>> >>>> algorithm, >>>>>> >>>>>> also >>>>>> protein sidechain orientation. >>>>>> >>>>>> Francesco >>>>>> >>>>>> >>>>>> 2012/10/4 rama david <[email protected]> >>>>>> >>>>>>> thank you Justin for reply. >>>>>>> >>>>>>> I dont know about long range interactions. >>>>>>> But as I freeze the group I think it will improve my computational >>>>> >>>>> speed. >>>>>>> >>>>>>> So is there any way to find out or decide which group should be >>>>>>> freeze, and which group should affect my interaction most probably?? >>>>>>> >>>>>>> Should I do Essential Dynamics ??? or Principle component analysis >>>> >>>> ??? >>>>>>> >>>>>>> >>>>>>> Would you suggest me any general protocol for such work?? >>>>>>> >>>>>>> Thank you in Advance >>>>>>> >>>>>>> >>>>>>> With Best Wishes and regards. >>>>>>> Rama David >>>>>>> >>>>>>> On Thu, Oct 4, 2012 at 3:57 PM, Justin Lemkul <[email protected]> >>>> >>>> wrote: >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/4/12 2:01 AM, rama david wrote: >>>>>>>> >>>>>>>>> Hi gromacs Friends, >>>>>>>>> I want to do peptide-receptor ( Protein) interaction >>>>>>>>> study.Receptor consist a single chain. >>>>>>>>> Peptide is made up of 4 amino acids. I know the interaction >>>>> >>>>> pattern >>>>>> >>>>>> of >>>>>>>>> >>>>>>>>> peptide and receptor. >>>>>>>>> I plan to mutate single residue each at a time and run 4 >>>>> >>>>> simulation . >>>>>>>>> >>>>>>>>> So I will have the 4 different simulation that contain the mutated >>>>>>>>> residues >>>>>>>>> and the wild one. >>>>>>>>> >>>>>>>>> >>>>>>>>> Then afterward from the interaction energy I want to select the >>>>>> >>>>>> peptide >>>>>>>>> >>>>>>>>> which is showing >>>>>>>>> stronger interaction than others. >>>>>>>>> >>>>>>>>> As mention I know the binding site, If I freeze the remaining >>>>> >>>>> portion >>>>>>> >>>>>>> in >>>>>>>>> >>>>>>>>> receptor >>>>>>>>> that not involved in binding , Is it going to affect my screening >>>>>>> >>>>>>> process >>>>>>>>> >>>>>>>>> ??? >>>>>>>>> >>>>>>>>> >>>>>>>> Potentially. Do you know that the binding interactions and the >>>>>> >>>>>> mutations >>>>>>>> >>>>>>>> will only perturb local residues? Do you know that there are no >>>>>>> >>>>>>> long-range >>>>>>>> >>>>>>>> motions to be considered? >>>>>>>> >>>>>>>> I think you gain very little by freezing portions of the system, >>>> >>>> and >>>>>> >>>>>> risk >>>>>>>> >>>>>>>> more than you gain. >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>> -- >>>>>>>> ==============================**========== >>>>>>>> >>>>>>>> Justin A. Lemkul, Ph.D. >>>>>>>> Research Scientist >>>>>>>> Department of Biochemistry >>>>>>>> Virginia Tech >>>>>>>> Blacksburg, VA >>>>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< >>>>>>> >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >>>>>>>> >>>>>>>> >>>>>>>> ==============================**========== >>>>>>>> -- >>>>>>>> gmx-users mailing list [email protected] >>>>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< >>>>>>> >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>>>>> >>>>>>>> * Please search the archive at http://www.gromacs.org/** >>>>>>>> Support/Mailing_Lists/Search< >>>>>>> >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! >>>>>>>> >>>>>>>> * Please don't post (un)subscribe requests to the list. Use the www >>>>>>>> interface or send it to [email protected]. >>>>>>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< >>>>>>> >>>>>>> http://www.gromacs.org/Support/Mailing_Lists> >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> gmx-users mailing list [email protected] >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>>> * Please search the archive at >>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>>>> www interface or send it to [email protected]. >>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Cordiali saluti, Dr.Oteri Francesco >>>>>> -- >>>>>> gmx-users mailing list [email protected] >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>> * Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>>> www interface or send it to [email protected]. >>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>> >>>>> -- >>>>> gmx-users mailing list [email protected] >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>> * Please search the archive at >>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>> * Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to [email protected]. >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>> >>>> >>>> >>>> -- >>>> >>>> ====================================================================== >>>> >>>> Thomas Evangelidis >>>> >>>> PhD student >>>> University of Athens >>>> Faculty of Pharmacy >>>> Department of Pharmaceutical Chemistry >>>> Panepistimioupoli-Zografou >>>> 157 71 Athens >>>> GREECE >>>> >>>> email: [email protected] >>>> >>>> [email protected] >>>> >>>> >>>> website: https://sites.google.com/site/thomasevangelidishomepage/ >>>> -- >>>> gmx-users mailing list [email protected] >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> * Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to [email protected]. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Shiyong Liu ------------------------------------------------------------------ Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China Tel：86-27-87558335-805 ------------------------------------------------------------------ Chinese Version: ------------------------------------------------------------------ 刘士勇 华中科技大学物理学院 生物物理模建小组 湖北省武汉市洪山区珞瑜路1037号 邮编：430074 电话：86-27-87558335-805 ------------------------------------------------------------------- -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
