[proteamdavis] FWD: Re: Various matters for the group
- From: "Tejal Pandya" <tgpandya@xxxxxxxxxxx>
- To: proteamdavis@xxxxxxxxxxxxx
- Date: Mon, 12 Jul 2004 12:58:12 -0700 (PDT)
Hey guys and gals,
We are meeting Benham TONIGHT (monday), at 6:30, at Kerr just like last
time. We can drive together again. He also sent me some info which I am
forwarding to you now. It is below in someone else's email to benham.
Tejal
Hi Tejal,
I have some information regarding protein surface calculations and
chameleon sequences. The former is the e-mail below, and the latter is in
the attached paper. Please forward this to everyone in the group. I hope
you have been successful in getting an account on our cluster. If not,
let
me know and I'll arrange with the SysAdmin.
Is the group intending to meet this evening?
Regards,
Craig
____________________________________________________
Hi, Craig-
First, let me address your questions. The calculation
of the solvent-
accessible surface of a protein from coordinates is one of
the classic problems
from the earliest days of computational biology. The
Richards algorithm, which
essentially involves rolling a water-molecule-sized sphere
over the protein and
determining which external atoms contact it, is the
corresponding classical
approach. Take a look at the following website:
http://www.netsci.org/Science/Compchem/feature14e.html
where there is a review of the topic, which may give the
information you need.
In answer to the second question, I'm attaching a paper
by Igor and myself,
which addresses the question of chameleon sequences from a
more general
perspective, and also includes references to the work in the
field. There is a
paper by Mihai Mezei, and one by Minor and Kim, which you
might want to
look at.
Regards,
Shelly
At 10:54 AM 6/24/2004 -0700, you wrote:
>Hi Dr. Benham,
>
>That sounds fine. We will meet you outside Kerr at 6:30pm on monday the
>28th. We can work out a better day for the following week to avoid July
>5th at that time.
>
>Looking forward to our meeting,
>
>Tejal
>
>
>
>
>
>
> > Hi Tejal,
> >
> > I was given keys that I was told would open the building, but I
have
> > never tried them. I'll verify that they do work, and then we can meet
> > there and then. The problem is, it may not be regarded as safe to
leave
> > the outside door unlocked for latecomers. Still, we can work these
>issues
> > out on Monday, at our first meeting.
> >
> > It may be a good idea to meet on a different day the following
> > week. I am unlikely to be able to make it on Monday July 5th.
> >
> >
> > Regards,
> > Craig
> >
> >
> >
> >
> > At 07:30 PM 6/23/2004 -0700, you wrote:
> >
> > >Dr. Benham,
> > >
> > >I spoke with some people in the undergrad office for Math and they
said
> > >that the commons room is available and that you have the key. The
> > >remaining problem is getting into Kerr Hall in the evening, because
the
> > >building is locked around 6pm. DO you a way of accessing a building
key?
> > >if so, then we are set for Mondays at 6:30pm.
> > >
> > >
> > >Tejal
> >
-- Attached file included as plaintext by Ecartis --
Hi Tejal,
I have some information regarding protein surface calculations and
chameleon sequences. The former is the e-mail below, and the latter is in
the attached paper. Please forward this to everyone in the group. I hope
you have been successful in getting an account on our cluster. If not, let
me know and I'll arrange with the SysAdmin.
Is the group intending to meet this evening?
Regards,
Craig
____________________________________________________
Hi, Craig-
First, let me address your questions. The calculation
of the solvent-
accessible surface of a protein from coordinates is one of
the classic problems
from the earliest days of computational biology. The
Richards algorithm, which
essentially involves rolling a water-molecule-sized sphere
over the protein and
determining which external atoms contact it, is the
corresponding classical
approach. Take a look at the following website:
http://www.netsci.org/Science/Compchem/feature14e.html
where there is a review of the topic, which may give the
information you need.
In answer to the second question, I'm attaching a paper
by Igor and myself,
which addresses the question of chameleon sequences from a
more general
perspective, and also includes references to the work in the
field. There is a
paper by Mihai Mezei, and one by Minor and Kim, which you
might want to
look at.
Regards,
Shelly
At 10:54 AM 6/24/2004 -0700, you wrote:
>Hi Dr. Benham,
>
>That sounds fine. We will meet you outside Kerr at 6:30pm on monday the
>28th. We can work out a better day for the following week to avoid July
>5th at that time.
>
>Looking forward to our meeting,
>
>Tejal
>
>
>
>
>
>
> > Hi Tejal,
> >
> > I was given keys that I was told would open the building, but I have
> > never tried them. I'll verify that they do work, and then we can meet
> > there and then. The problem is, it may not be regarded as safe to leave
> > the outside door unlocked for latecomers. Still, we can work these
>issues
> > out on Monday, at our first meeting.
> >
> > It may be a good idea to meet on a different day the following
> > week. I am unlikely to be able to make it on Monday July 5th.
> >
> >
> > Regards,
> > Craig
> >
> >
> >
> >
> > At 07:30 PM 6/23/2004 -0700, you wrote:
> >
> > >Dr. Benham,
> > >
> > >I spoke with some people in the undergrad office for Math and they said
> > >that the commons room is available and that you have the key. The
> > >remaining problem is getting into Kerr Hall in the evening, because the
> > >building is locked around 6pm. DO you a way of accessing a building key?
> > >if so, then we are set for Mondays at 6:30pm.
> > >
> > >
> > >Tejal
> >
-- Binary/unsupported file stripped by Ecartis --
-- Type: APPLICATION/PDF
-- Desc: Flexibility.pdf
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