subject:"\[gmx\-users\] Re\: Folding rate"

Re: [gmx-users] Re: Folding rate

2012-01-04 Thread David van der Spoel

Check Phys Rev Let 96 (2006) art nr 238102. You need simulations with 
reproducible folding so small peptides only. 

Tot Ziens!


Op 4 jan 2012 om 02:35 heeft bharat gupta  het 
volgende geschreven:

> Thanks for all your replies. I want to know this can be done in gromacs or 
> not - using REMD with structure based models generated from SMOG server to 
> study protein folding and unfolding ??. Also, I have a question about how to 
> determine  the exchange probablities for a particular REMD experiment and 
> also how many replicas do we need to consider, does that depend on the 
> temperature list generated from the T_REMD server??
> 
> On Sat, Dec 31, 2011 at 11:36 AM, felmer...@uchile.cl  
> wrote:
> Yeah sure. There are several methods to trick your peptide to fold, but often 
> you loose the real kinetics by using them. I think a 230 residues protein is 
> too big to study folding kinetics through MD (because of the folding 
> kinetics, not the size of the system). With topology based potenitials 
> (Go-like models) you surely can do it, but take into account the the core 
> asumption there is that the energy landscape of your peptide is perfectly 
> funneled to the native state, which is a very good approximation for small 
> protein (like a 100 residues) but not so nice for bigger proteins. In fact, 
> even small proteins have intermediate states which makes the energy landscape 
> somehow rugged (the engrailed homeodomain, the trp repressor, etc). Besides 
> that, it is not a trivial task to go from the reduced representation to real 
> kinetic constants. Maybe if you are interested in comparison rather than 
> absolute values you can be lucky with the Go-modeling. If that is the case 
> maybe you should try the SMOG potential it is very fast.
> 
>  
> 
> regards
> 
> Mensaje original
> De: bharat.85.m...@gmail.com
> Fecha: 30-dic-2011 22:45
> 
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] Re: Folding rate
> 
> The protein that I am dealing with is a 230 amino acid protein. I have come 
> across some methods that used reduced space model of protein such as CABS for 
> locating the protein folding pathway. An another paper describes about using 
> Go model together with Rigid body dynamics for finding protein folding 
> pathway. 
> 
> On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl  
> wrote:
> I small thing to consider with that particular paper is that DE Shaw has a 
> special machine (Anton) to do those calculations, so in principle it is not 
> possible to reproduce them (in a reasonable amount of time) on a regular 
> (super)computer. I think your best shot, if your protein is small enough, is 
> to use accelerated MD mixed with some good old kramer's theory. See for 
> example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581.
> 
> In any case it seems to me like too much of an effort, in the end here you 
> really rely in the accuracy of the forcefield.
> 
> Regards
> 
> 
> Mensaje original
> De: jmda...@itqb.unl.pt
> Fecha: 30-dic-2011 21:40
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] Re: Folding rate
> 
> 
> As it was pointed out, the literature is vast on this subject.
> 
> Moreover, calculating folding rates from simulations is not a trivial 
> subject, and it relies on many assumptions (e.g. what is considered "folded", 
> that the sampling obtained is enough). Even for small peptides, "enough 
> sampling" may mean several hundreds of microsseconds, something not 
> accessible to everyone.
> 
> For a very recent article on the subject, check out:
> 
> Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How 
> Fast-Folding Proteins Fold, Science 334:517-520.
> http://dx.doi.org/10.1126/science.1208351
> 
> Regards,
> João
> 
> On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi  wrote:
> As Justin pointed out, there is a vast literature on this topic, you need to 
> ask yourself what you seek, and look at many review articles to find some 
> reasonable starting points for you own needs and designs. Beyond that, it's a 
> lot of hard work...
> 
> On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
> 
> Thanks for your advice... Could you please refer me some papers regarding 
> this 
> 
> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi  wrote:
> No, there is no way to use such data to determine the folding rate of the 
> intact protein. If you used a fragment approach you could potentially (read 
> lots of papers on REMD) isolate nucleation sites, but minus the tertiary 
> interaction scheme you could not tell a compelling story. Now, if you want to 
> find nucleation sites a

Re: [gmx-users] Re: Folding rate

2012-01-03 Thread felmer...@uchile.cl


Actually i know people using Go-models to study protein folding for proteins as 
large as 300 aa. Now, in these cases you need to use biasing potentials and not 
temperature exchages (maybe both?). In principle, the REMD will help you with 
the comformational exchange but it also includes a new level of complexity 
since the temperature distribution for the correct exchange ratios is pretty 
much an empiric issue. In principle, there is no problem to run these 
simulations independently and then combining them by WHAM taking the 
temperature as the only bias. Just consider the parallel tempering as a 
sampling enhancer the same way as it is used also with hamiltonian hopping.

 

If you go for the umbrella sampling way you can use the PLUMED plugin for 
colective variables. There you can apply a bias directly to the number of 
contacts of the structure (a contact map bias) or maybe to the gyration radius. 
In principle, once you unbias your histograms you can calculate the free energy 
profile of any colective variable using a "multidimensional histogram" trick. 
In the end, what you need to now is how much energy you are adding to sample 
that state. 

 

Once you have the free energy profile at the folding temperature (this also 
needs some trial and error) you should be able to measure the height of the 
energetic barrier between states which is in principle what determines that 
transition rates. 

 

As mark said, there are tons of papers of this as "Go-models" ar practically 
the only way people had to explore the protein folding thermodynamics in the 
computer.

 

regards

 

Felipe
Mensaje originalDe: mark.abra...@anu.edu.auFecha: 03-ene-2012 
22:52Para: "Discussion list for GROMACS users"Asunto: 
Re: [gmx-users] Re: Folding rateOn 4/01/2012 12:35 PM, bharat gupta wrote:> 
Thanks for all your replies. I want to know this can be done in > gromacs or 
not - using REMD with structure based models generated from > SMOG server to 
study protein folding and unfolding ??.Well, it can be done, but you probably 
don't have enough computer to fold a 230 residue protein at atomistic 
resolution (or maybe even coarse-grained).> Also, I have a question about how 
to determine  the exchange > probablities for a particular REMD experiment and 
also how many > replicas do we need to consider, does that depend on the 
temperature > list generated from the T_REMD server??There's a significant 
literature on these subjects. I suggest you read some of it. Short answer: pick 
the highest temperature according to the size of the largest barrier you expect 
to cross (good luck guessing that), have around 20% exchange acceptance, and be 
prepared to observe where the replica-flow bottle necks are and to iteratively 
refine you temperatures.Mark-- gmx-users mailing list
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Re: [gmx-users] Re: Folding rate

2012-01-03 Thread bharat gupta

Thanks for the reply. Since I need to study the effect of beta-hairpin turn
design on protein folding . I thought that first unfolding and then
refolding would give the change in folding time. As you told that to do
such a task would require large computational power. Is there any other
method in MDS that could be used ??

On Wed, Jan 4, 2012 at 10:52 AM, Mark Abraham wrote:

> On 4/01/2012 12:35 PM, bharat gupta wrote:
>
>> Thanks for all your replies. I want to know this can be done in gromacs
>> or not - using REMD with structure based models generated from SMOG server
>> to study protein folding and unfolding ??.
>>
>
> Well, it can be done, but you probably don't have enough computer to fold
> a 230 residue protein at atomistic resolution (or maybe even
> coarse-grained).
>
>
>  Also, I have a question about how to determine  the exchange probablities
>> for a particular REMD experiment and also how many replicas do we need to
>> consider, does that depend on the temperature list generated from the
>> T_REMD server??
>>
>
> There's a significant literature on these subjects. I suggest you read
> some of it. Short answer: pick the highest temperature according to the
> size of the largest barrier you expect to cross (good luck guessing that),
> have around 20% exchange acceptance, and be prepared to observe where the
> replica-flow bottle necks are and to iteratively refine you temperatures.
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Re: Folding rate

2012-01-03 Thread Mark Abraham


On 4/01/2012 12:35 PM, bharat gupta wrote:
Thanks for all your replies. I want to know this can be done in 
gromacs or not - using REMD with structure based models generated from 
SMOG server to study protein folding and unfolding ??.


Well, it can be done, but you probably don't have enough computer to 
fold a 230 residue protein at atomistic resolution (or maybe even 
coarse-grained).


Also, I have a question about how to determine  the exchange 
probablities for a particular REMD experiment and also how many 
replicas do we need to consider, does that depend on the temperature 
list generated from the T_REMD server??


There's a significant literature on these subjects. I suggest you read 
some of it. Short answer: pick the highest temperature according to the 
size of the largest barrier you expect to cross (good luck guessing 
that), have around 20% exchange acceptance, and be prepared to observe 
where the replica-flow bottle necks are and to iteratively refine you 
temperatures.


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Re: Folding rate

2012-01-03 Thread bharat gupta

Thanks for all your replies. I want to know this can be done in gromacs or
not - using REMD with structure based models generated from SMOG server to
study protein folding and unfolding ??. Also, I have a question about how
to determine  the exchange probablities for a particular REMD experiment
and also how many replicas do we need to consider, does that depend on the
temperature list generated from the T_REMD server??

On Sat, Dec 31, 2011 at 11:36 AM, felmer...@uchile.cl
wrote:

> Yeah sure. There are several methods to trick your peptide to fold, but
> often you loose the real kinetics by using them. I think a 230 residues
> protein is too big to study folding kinetics through MD (because of the
> folding kinetics, not the size of the system). With topology based
> potenitials (Go-like models) you surely can do it, but take into account
> the the core asumption there is that the energy landscape of your peptide
> is perfectly funneled to the native state, which is a very good
> approximation for small protein (like a 100 residues) but not so nice for
> bigger proteins. In fact, even small proteins have intermediate states
> which makes the energy landscape somehow rugged (the engrailed homeodomain,
> the trp repressor, etc). Besides that, it is not a trivial task to go from
> the reduced representation to real kinetic constants. Maybe if you are
> interested in comparison rather than absolute values you can be lucky with
> the Go-modeling. If that is the case maybe you should try the SMOG
> potential it is very fast.
>
>
>
> regards
>
> Mensaje original
> De: bharat.85.m...@gmail.com
> Fecha: 30-dic-2011 22:45
>
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] Re: Folding rate
>
> The protein that I am dealing with is a 230 amino acid protein. I have
> come across some methods that used reduced space model of protein such as
> CABS for locating the protein folding pathway. An another paper describes
> about using Go model together with Rigid body dynamics for finding protein
> folding pathway.
>
> On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl  > wrote:
>
>> I small thing to consider with that particular paper is that DE Shaw has
>> a special machine (Anton) to do those calculations, so in principle it is
>> not possible to reproduce them (in a reasonable amount of time) on a
>> regular (super)computer. I think your best shot, if your protein is small
>> enough, is to use accelerated MD mixed with some good old kramer's theory.
>> See for example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581.
>>
>> In any case it seems to me like too much of an effort, in the end here
>> you really rely in the accuracy of the forcefield.
>>
>> Regards
>>
>>
>> Mensaje original
>> De: jmda...@itqb.unl.pt
>> Fecha: 30-dic-2011 21:40
>> Para: "Discussion list for GROMACS users"
>> Asunto: Re: [gmx-users] Re: Folding rate
>>
>>
>> As it was pointed out, the literature is vast on this subject.
>>
>>
>> Moreover, calculating folding rates from simulations is not a trivial
>> subject, and it relies on many assumptions (e.g. what is considered
>> "folded", that the sampling obtained is enough). Even for small peptides,
>> "enough sampling" may mean several hundreds of microsseconds, something not
>> accessible to everyone.
>>
>> For a very recent article on the subject, check out:
>>
>> Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How
>> Fast-Folding Proteins Fold, *Science* 334:517-520.
>> http://dx.doi.org/10.1126/science.1208351
>>
>> Regards,
>> João
>>
>> On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:
>>
>>>  As Justin pointed out, there is a vast literature on this topic, you
>>> need to ask yourself what you seek, and look at many review articles to
>>> find some reasonable starting points for you own needs and designs. Beyond
>>> that, it's a lot of hard work...
>>>
>>>  On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>>>
>>> Thanks for your advice... Could you please refer me some papers
>>> regarding this 
>>>
>>> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi wrote:
>>>
>>>> No, there is no way to use such data to determine the folding rate of
>>>> the intact protein. If you used a fragment approach you could potentially
>>>> (read lots of papers on REMD) isolate nucleation sites, but minus the
>>>> tertiary interaction scheme you could not tell a compelling story. Now, if
>>>> you want

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread felmer...@uchile.cl

Yeah sure. There are several methods to trick your peptide to fold, but often
you loose the real kinetics by using them. I think a 230 residues protein is
too big to study folding kinetics through MD (because of the folding kinetics,
not the size of the system). With topology based potenitials (Go-like models)
you surely can do it, but take into account the the core asumption there is
that the energy landscape of your peptide is perfectly funneled to the native
state, which is a very good approximation for small protein (like a 100
residues) but not so nice for bigger proteins. In fact, even small proteins
have intermediate states which makes the energy landscape somehow rugged (the
engrailed homeodomain, the trp repressor, etc). Besides that, it is not a
trivial task to go from the reduced representation to real kinetic constants.
Maybe if you are interested in comparison rather than absolute values you can
be lucky with the Go-modeling. If that is the case maybe you should try the
SMOG potential it is very fast.

regards
Mensaje original De: bharat.85.m...@gmail.com Fecha: 30-dic-2011 22:45
Para: "Discussion list for GROMACS users" Asunto: Re:
[gmx-users] Re: Folding rate The protein that I am dealing with is a 230 amino
acid protein. I have come across some methods that used reduced space model of
protein such as CABS for locating the protein folding pathway. An another paper
describes about using Go model together with Rigid body dynamics for finding
protein folding pathway.
On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl
wrote:

I small thing to consider with that particular paper is that DE Shaw has a
special machine (Anton) to do those calculations, so in principle it is not
possible to reproduce them (in a reasonable amount of time) on a regular
(super)computer. I think your best shot, if your protein is small enough, is to
use accelerated MD mixed with some good old kramer's theory. See for example J.
Chem. Theory Comput., 2011, 7 (3), pp 575–581.

In any case it seems to me like too much of an effort, in the end here you
really rely in the accuracy of the forcefield.

Regards

Mensaje original De: jmda...@itqb.unl.pt Fecha: 30-dic-2011 21:40 Para:
"Discussion list for GROMACS users" Asunto: Re:
[gmx-users] Re: Folding rate

As it was pointed out, the literature is vast on this subject.

Moreover, calculating folding rates from simulations is not a trivial subject,
and it relies on many assumptions (e.g. what is considered "folded", that the
sampling obtained is enough). Even for small peptides, "enough sampling" may
mean several hundreds of microsseconds, something not accessible to everyone.

For a very recent article on the subject, check out:

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding
Proteins Fold, Science 334:517-520.
http://dx.doi.org/10.1126/science.1208351

Regards,
João

On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:

As Justin pointed out, there is a vast literature on this topic, you need to
ask yourself what you seek, and look at many review articles to find some
reasonable starting points for you own needs and designs. Beyond that, it's a
lot of hard work...

On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:

Thanks for your advice... Could you please refer me some papers regarding this

On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi wrote:
No, there is no way to use such data to determine the folding rate of the
intact protein. If you used a fragment approach you could potentially (read
lots of papers on REMD) isolate nucleation sites, but minus the tertiary
interaction scheme you could not tell a compelling story. Now, if you want to
find nucleation sites and see if there are spatially proximal sites and
simulate them together... You might begin to tell a story. Ken

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread bharat gupta

The protein that I am dealing with is a 230 amino acid protein. I have come
across some methods that used reduced space model of protein such as CABS
for locating the protein folding pathway. An another paper describes about
using Go model together with Rigid body dynamics for finding protein
folding pathway.

On Sat, Dec 31, 2011 at 10:23 AM, felmer...@uchile.cl
wrote:

> I small thing to consider with that particular paper is that DE Shaw has a
> special machine (Anton) to do those calculations, so in principle it is not
> possible to reproduce them (in a reasonable amount of time) on a regular
> (super)computer. I think your best shot, if your protein is small enough,
> is to use accelerated MD mixed with some good old kramer's theory. See for
> example J. Chem. Theory Comput., 2011, 7 (3), pp 575–581.
>
> In any case it seems to me like too much of an effort, in the end here you
> really rely in the accuracy of the forcefield.
>
> Regards
>
>
> Mensaje original
> De: jmda...@itqb.unl.pt
> Fecha: 30-dic-2011 21:40
> Para: "Discussion list for GROMACS users"
> Asunto: Re: [gmx-users] Re: Folding rate
>
>
> As it was pointed out, the literature is vast on this subject.
>
>
> Moreover, calculating folding rates from simulations is not a trivial
> subject, and it relies on many assumptions (e.g. what is considered
> "folded", that the sampling obtained is enough). Even for small peptides,
> "enough sampling" may mean several hundreds of microsseconds, something not
> accessible to everyone.
>
> For a very recent article on the subject, check out:
>
> Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How
> Fast-Folding Proteins Fold, *Science* 334:517-520.
> http://dx.doi.org/10.1126/science.1208351
>
> Regards,
> João
>
> On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:
>
>>  As Justin pointed out, there is a vast literature on this topic, you
>> need to ask yourself what you seek, and look at many review articles to
>> find some reasonable starting points for you own needs and designs. Beyond
>> that, it's a lot of hard work...
>>
>>  On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>>
>> Thanks for your advice... Could you please refer me some papers regarding
>> this 
>>
>> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi wrote:
>>
>>> No, there is no way to use such data to determine the folding rate of
>>> the intact protein. If you used a fragment approach you could potentially
>>> (read lots of papers on REMD) isolate nucleation sites, but minus the
>>> tertiary interaction scheme you could not tell a compelling story. Now, if
>>> you want to find nucleation sites and see if there are spatially proximal
>>> sites and simulate them together... You might begin to tell a story.
>>>
>>> Ken
>>>
>>>
>>> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
>>>
>>>
>>>>
>>>> bharat gupta wrote:
>>>>
>>>>> Thanks for your reply. I want to whether does it make any sense or is
>>>>> it possible to simulate fragments of proteins and find their folding rate
>>>>> and then correlate it to folding rate of whole protein ??
>>>>>
>>>>
>>>> Simulating arbitrary parts of a protein may or may not produce any
>>>> relevant information, likely the latter.  Independently folding domains
>>>> might be simulated in isolation, but if there is a chance that the peptide
>>>> sequences have any effect on neighboring residues or even more distal
>>>> sites, you'll never produce anything useful.
>>>>
>>>> -Justin
>>>>
>>>> On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul >>>> jalem...@vt.edu>> wrote:
>>>>>   bharat gupta wrote:
>>>>>   Hi,
>>>>>   I want to know whether it's possible to calculate the folding
>>>>>   rate of 20 residue peptide folding into a beta-hairpin using
>>>>>   gromacs ??
>>>>>   Anything is possible ;)  But seriously, there is existing literature
>>>>>   on such topics, I suspect you can find methodology that will suit
>>>>>   your needs.
>>>>>   -Justin
>>>>>   -- ==__==
>>>>>   Justin A. Lemkul
>>>>>   Ph.D. Candidate
>>>>>   ICTAS Doctoral Scholar
>>>>>   MILES-IGERT Trainee
>>>>>   Department of Biochemistry
&

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread felmer...@uchile.cl

In any case it seems to me like too much of an effort, in the end here you
really rely in the accuracy of the forcefield.

Regards

Mensaje original De: jmda...@itqb.unl.pt Fecha: 30-dic-2011 21:40 Para:
"Discussion list for GROMACS users" Asunto: Re:
[gmx-users] Re: Folding rate As it was pointed out, the literature is vast on
this subject.

For a very recent article on the subject, check out:

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How Fast-Folding
Proteins Fold, Science 334:517-520.
http://dx.doi.org/10.1126/science.1208351

Regards,
João

On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:

On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:

Thanks for your advice... Could you please refer me some papers regarding this

On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
bharat gupta wrote:
Thanks for your reply. I want to whether does it make any sense or is it
possible to simulate fragments of proteins and find their folding rate and then
correlate it to folding rate of whole protein ??
Simulating arbitrary parts of a protein may or may not produce any relevant
information, likely the latter. Independently folding domains might be
simulated in isolation, but if there is a chance that the peptide sequences
have any effect on neighboring residues or even more distal sites, you'll never
produce anything useful. -Justin
On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote: bharat gupta wrote: Hi, I want
to know whether it's possible to calculate the folding rate of 20 residue
peptide folding into a beta-hairpin using gromacs ?? Anything is
possible ;) But seriously, there is existing literature on such topics, I
suspect you can find methodology that will suit your needs. -Justin --
==__== Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of
Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu
<http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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ICTAS Doctoral Scholar MILE

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread João M . Damas

As it was pointed out, the literature is vast on this subject.

Moreover, calculating folding rates from simulations is not a trivial
subject, and it relies on many assumptions (e.g. what is considered
"folded", that the sampling obtained is enough). Even for small peptides,
"enough sampling" may mean several hundreds of microsseconds, something not
accessible to everyone.

For a very recent article on the subject, check out:

Lindorff-Larsen, K., Piana, S., Dror, R.O., Shaw, D.E. (2011) How
Fast-Folding Proteins Fold, *Science* 334:517-520.
http://dx.doi.org/10.1126/science.1208351

Regards,
João

On Sat, Dec 31, 2011 at 12:19 AM, KS Rotondi wrote:

> As Justin pointed out, there is a vast literature on this topic, you need
> to ask yourself what you seek, and look at many review articles to find
> some reasonable starting points for you own needs and designs. Beyond that,
> it's a lot of hard work...
>
> On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:
>
> Thanks for your advice... Could you please refer me some papers regarding
> this 
>
> On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi wrote:
>
>> No, there is no way to use such data to determine the folding rate of the
>> intact protein. If you used a fragment approach you could potentially (read
>> lots of papers on REMD) isolate nucleation sites, but minus the tertiary
>> interaction scheme you could not tell a compelling story. Now, if you want
>> to find nucleation sites and see if there are spatially proximal sites and
>> simulate them together... You might begin to tell a story.
>>
>> Ken
>>
>>
>> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
>>
>>
>>>
>>> bharat gupta wrote:
>>>
 Thanks for your reply. I want to whether does it make any sense or is
 it possible to simulate fragments of proteins and find their folding rate
 and then correlate it to folding rate of whole protein ??

>>>
>>> Simulating arbitrary parts of a protein may or may not produce any
>>> relevant information, likely the latter.  Independently folding domains
>>> might be simulated in isolation, but if there is a chance that the peptide
>>> sequences have any effect on neighboring residues or even more distal
>>> sites, you'll never produce anything useful.
>>>
>>> -Justin
>>>
>>>  On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul >>> jalem...@vt.edu>> wrote:
   bharat gupta wrote:
   Hi,
   I want to know whether it's possible to calculate the folding
   rate of 20 residue peptide folding into a beta-hairpin using
   gromacs ??
   Anything is possible ;)  But seriously, there is existing literature
   on such topics, I suspect you can find methodology that will suit
   your needs.
   -Justin
   -- ==**__==
   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   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 listgmx-users@gromacs.org
   
   
 http://lists.gromacs.org/__**mailman/listinfo/gmx-users
   
 
 >
   Please search the archive at
   
 http://www.gromacs.org/__**Support/Mailing_Lists/Search
   
 >
 before posting!
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 >
 --
 Bharat
 Ph.D. Candidate
 Room No. : 7202A, 2nd Floor
 Biomolecular Engineering Laboratory
 Division of Chemical Engineering and Polymer Science
 Pusan National University
 Busan -609735
 South Korea
 Lab phone no. - +82-51-510-3680, +82-51-583-8343
 Mobile no. - 010-5818-3680
 E-mail : monu46...@yahoo.com 

>>>
>>> --
>>> ==**==
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of B

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread KS Rotondi

As Justin pointed out, there is a vast literature on this topic, you  
need to ask yourself what you seek, and look at many review articles  
to find some reasonable starting points for you own needs and designs.  
Beyond that, it's a lot of hard work...

On Dec 30, 2011, at 7:04 PM, bharat gupta wrote:

Thanks for your advice... Could you please refer me some papers  
regarding this 


On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi  
 wrote:
No, there is no way to use such data to determine the folding rate  
of the intact protein. If you used a fragment approach you could  
potentially (read lots of papers on REMD) isolate nucleation sites,  
but minus the tertiary interaction scheme you could not tell a  
compelling story. Now, if you want to find nucleation sites and see  
if there are spatially proximal sites and simulate them together...  
You might begin to tell a story.


Ken


On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:



bharat gupta wrote:
Thanks for your reply. I want to whether does it make any sense or  
is it possible to simulate fragments of proteins and find their  
folding rate and then correlate it to folding rate of whole protein ??


Simulating arbitrary parts of a protein may or may not produce any  
relevant information, likely the latter.  Independently folding  
domains might be simulated in isolation, but if there is a chance  
that the peptide sequences have any effect on neighboring residues  
or even more distal sites, you'll never produce anything useful.


-Justin

On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul mailto:jalem...@vt.edu 
>> wrote:

  bharat gupta wrote:
  Hi,
  I want to know whether it's possible to calculate the folding
  rate of 20 residue peptide folding into a beta-hairpin using
  gromacs ??
  Anything is possible ;)  But seriously, there is existing literature
  on such topics, I suspect you can find methodology that will suit
  your needs.
  -Justin
  -- ==__==
  Justin A. Lemkul
  Ph.D. Candidate
  ICTAS Doctoral Scholar
  MILES-IGERT Trainee
  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 listgmx-users@gromacs.org
  
  http://lists.gromacs.org/__mailman/listinfo/gmx-users
  
  Please search the archive at
  http://www.gromacs.org/__Support/Mailing_Lists/Search
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  interface or send it to gmx-users-requ...@gromacs.org
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com

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Re: [gmx-users] Re: Folding rate

2011-12-30 Thread KS Rotondi


Dear Bharat,

20 residue peptides in general don't fold, they inhabit a  
conformational space. Can you determine the fraction of time spent in  
a near native (as defined by you) conformation under given conditions  
to within the ability of the force field, yes, you can. To calculate a  
true rate of folding, if you were studying, say, the trp cage protein  
(20 AA, defined tertiary structure), you'd have to start with a  
primarily beta or helix chain (use a primary sequence secondary  
structure predictor to assign starting conformations) as would be  
expected to emerge from the ribosome, simulate until a native-like  
conformation was formed, and repeat many times until a statistically  
reasonable answer was approached, and even then, for something that  
small, I'd bet it spends a fair amount of time in non-native  
conformations.


Many times.

Ken

Dr. K.S. Rotondi
Departments of Chemistry, Biochemistry and Molecular Biology
The University of Massachusetts - Amherst
Amherst, MA 01003

"If there's a solution, why worry?, If there's no solution, why worry?"
His Holiness, the Dalai Llama



On Dec 30, 2011, at 5:39 PM, bharat gupta wrote:


Hi,

I want to know whether it's possible to calculate the folding rate  
of 20 residue peptide folding into a beta-hairpin using gromacs ??


--
Bharat

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Re: [gmx-users] Re: Folding rate

2011-12-30 Thread bharat gupta

Thanks for your advice... Could you please refer me some papers regarding
this 

On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi  wrote:

> No, there is no way to use such data to determine the folding rate of the
> intact protein. If you used a fragment approach you could potentially (read
> lots of papers on REMD) isolate nucleation sites, but minus the tertiary
> interaction scheme you could not tell a compelling story. Now, if you want
> to find nucleation sites and see if there are spatially proximal sites and
> simulate them together... You might begin to tell a story.
>
> Ken
>
>
> On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:
>
>
>>
>> bharat gupta wrote:
>>
>>> Thanks for your reply. I want to whether does it make any sense or is it
>>> possible to simulate fragments of proteins and find their folding rate and
>>> then correlate it to folding rate of whole protein ??
>>>
>>
>> Simulating arbitrary parts of a protein may or may not produce any
>> relevant information, likely the latter.  Independently folding domains
>> might be simulated in isolation, but if there is a chance that the peptide
>> sequences have any effect on neighboring residues or even more distal
>> sites, you'll never produce anything useful.
>>
>> -Justin
>>
>>  On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>   bharat gupta wrote:
>>>   Hi,
>>>   I want to know whether it's possible to calculate the folding
>>>   rate of 20 residue peptide folding into a beta-hairpin using
>>>   gromacs ??
>>>   Anything is possible ;)  But seriously, there is existing literature
>>>   on such topics, I suspect you can find methodology that will suit
>>>   your needs.
>>>   -Justin
>>>   -- ==**__==
>>>   Justin A. Lemkul
>>>   Ph.D. Candidate
>>>   ICTAS Doctoral Scholar
>>>   MILES-IGERT Trainee
>>>   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 listgmx-users@gromacs.org
>>>   
>>>   
>>> 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 gmx-users-requ...@gromacs.org
>>>   >> >.
>>>   Can't post? Read 
>>> http://www.gromacs.org/__**Support/Mailing_Lists
>>>   
>>> 
>>> >
>>> --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46...@yahoo.com 
>>>
>>
>> --
>> ==**==
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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 listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists

Re: [gmx-users] Re: Folding rate

2011-12-30 Thread KS Rotondi

No, there is no way to use such data to determine the folding rate of  
the intact protein. If you used a fragment approach you could  
potentially (read lots of papers on REMD) isolate nucleation sites,  
but minus the tertiary interaction scheme you could not tell a  
compelling story. Now, if you want to find nucleation sites and see if  
there are spatially proximal sites and simulate them together... You  
might begin to tell a story.


Ken

On Dec 30, 2011, at 6:09 PM, Justin A. Lemkul wrote:




bharat gupta wrote:
Thanks for your reply. I want to whether does it make any sense or  
is it possible to simulate fragments of proteins and find their  
folding rate and then correlate it to folding rate of whole  
protein ??


Simulating arbitrary parts of a protein may or may not produce any  
relevant information, likely the latter.  Independently folding  
domains might be simulated in isolation, but if there is a chance  
that the peptide sequences have any effect on neighboring residues  
or even more distal sites, you'll never produce anything useful.


-Justin

On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul mailto:jalem...@vt.edu 
>> wrote:

   bharat gupta wrote:
   Hi,
   I want to know whether it's possible to calculate the folding
   rate of 20 residue peptide folding into a beta-hairpin using
   gromacs ??
   Anything is possible ;)  But seriously, there is existing  
literature

   on such topics, I suspect you can find methodology that will suit
   your needs.
   -Justin
   -- ==__==
   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   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 listgmx-users@gromacs.org
   
   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 gmx-users-requ...@gromacs.org
   .
   Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
   
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Re: Folding rate

2011-12-30 Thread Justin A. Lemkul




bharat gupta wrote:
Thanks for your reply. I want to whether does it make any sense or is it 
possible to simulate fragments of proteins and find their folding rate 
and then correlate it to folding rate of whole protein ??




Simulating arbitrary parts of a protein may or may not produce any relevant 
information, likely the latter.  Independently folding domains might be 
simulated in isolation, but if there is a chance that the peptide sequences have 
any effect on neighboring residues or even more distal sites, you'll never 
produce anything useful.


-Justin

On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul > wrote:




bharat gupta wrote:

Hi,

I want to know whether it's possible to calculate the folding
rate of 20 residue peptide folding into a beta-hairpin using
gromacs ??


Anything is possible ;)  But seriously, there is existing literature
on such topics, I suspect you can find methodology that will suit
your needs.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 listgmx-users@gromacs.org


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.
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] Re: Folding rate

2011-12-30 Thread bharat gupta

Thanks for your reply. I want to whether does it make any sense or is it
possible to simulate fragments of proteins and find their folding rate and
then correlate it to folding rate of whole protein ??

On Sat, Dec 31, 2011 at 8:00 AM, Justin A. Lemkul  wrote:

>
>
> bharat gupta wrote:
>
>> Hi,
>>
>> I want to know whether it's possible to calculate the folding rate of 20
>> residue peptide folding into a beta-hairpin using gromacs ??
>>
>>
> Anything is possible ;)  But seriously, there is existing literature on
> such topics, I suspect you can find methodology that will suit your needs.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] Re: Folding rate

2011-12-30 Thread Justin A. Lemkul




bharat gupta wrote:

Hi,

I want to know whether it's possible to calculate the folding rate of 20 
residue peptide folding into a beta-hairpin using gromacs ??




Anything is possible ;)  But seriously, there is existing literature on such 
topics, I suspect you can find methodology that will suit your needs.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: Folding rate

2011-12-30 Thread bharat gupta

Hi,

I want to know whether it's possible to calculate the folding rate of 20
residue peptide folding into a beta-hairpin using gromacs ??

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Bharat
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Re: [gmx-users] Re: Folding rate

Re: [gmx-users] Re: Folding rate

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[gmx-users] Re: Folding rate

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