Nabble - Bio.net - Molmodel

What is your favorite journal in the field of computational structural biology?

2009-04-25T08:13:37Z

Following the success of our previous poll which was followed by an extensive and interesting discussion, and in order to better our Bi(Tri,..)-Weekly Digests, we present a new poll which will determine once and for all, which is the best journal for the computational structural biologist.

http://rosettadesigngroup.com/blog/353/what-is-your-favorite-journal-in-the-field-of-computational-structural-biology/

Of course we’re all reading all of the journals mentioned, and certainly each has its own benefits. There is also the question if by “favorite” journal we mean where would you like to publish, or which are you enjoying reading the most? We know the question isn’t adequately defined. Nontheless, we urge you to pick one and try to explain in the comments what makes that journal special.

Nir London.

http://rosettadesigngroup.com/blog/

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Molecular Modeling in Drug Design: New Learning Resource

2009-03-15T02:13:33Z

The new Molecular Conceptor Learning Series has been released - a new
series of computer-based training modules that have been designed to
give researchers in the field of drug design, the comprehensive

knowledge necessary to succeed in their daily, virtual drug design tasks.

The five modules that make up the Molecular Conceptor Learning Series are:

     * Drug Design
     * Cheminformatics
     * Medicinal Chemistry

     * Structural Bioinformatics
     * Practical Drug Discovery: Case Studies

For more information visit: http://www.drugdesign.com

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Computational Chemistry at Bio-IT conference

2009-03-03T11:19:27Z

-

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Summer Training

2009-02-16T04:04:44Z

NeoGen Bio Solutions Offer Summer Project & Intensive industrial
training Program

Special features:

• Special job opportunities for training students at NeoGen
• Guidance for PhD & studies in abroad
• Hands on training on commercial softwares in addition to the
training program

Intensive Industrial Training Program Duration 15 days:

• Introduction to Bioinformatics
• Genomic tools and databases
• Immunoinformatics
• Metabolomics
• Microarray Data Analysis.
• Molecular Modeling and Drug Design
• Perl Programming
• Proteomic tools and Databases
• Python Programming
• Structural Bioinformatics

Summer Project+Traning 1 Month:

• BIOTOOLS AND SOFTWARES
• BIOPROGRAMMING
• DATABASE CREATION
• GENOMICS
• PROTEOMICS
• STRUCTURAL BIOLOGY
• DRUG DESIGNING
• COMPUTATIONAL BIOLOGY

NeoGen Biosolutions,
12, M.E.S.Road, Ganapathipuram
(Behind Madras Christian College)
East Thambaram, Chennai-59
9094019566, 9094019577
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Molecular Modelling and Structure-based Drug Design - deadline reminder

2009-02-02T13:31:30Z

This is a reminder for those people considering taking our online
course, which begins again in March 2009.

The application deadline is 13 February. However, it is advisable to
apply before the deadline to allow time for any questions in processing
your application.

I have included the course outline below; the full details are on our
website
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6251.html). If
you have any questions, or need advice on the module options, please
contact Heather.Vincent@...

This course is divided into 7 sections as follows:-

1. Molecular Mechanics
a. The molecular potential energy function
b. The empirical force field
c. Sources of force field data
d. Some examples of important force fields

2. Energy Minimisation
a. First derivative techniques: steepest descent and conjugate
gradients
b. Second derivative techniques: Hessian matrix and Newton-Raphson
c. Global optimisation (simulated annealing, Tabu search, genetic
algorithms)

3. Molecular Dynamics and Monte Carlo Simulations
a. Brief introduction to statistical mechanics
b. Molecular dynamics simulations
c. Monte Carlo simulations

4. Conformational Analysis
a. Systematic methods
b. Random search methods
c. Distance geometry
d. Molecular dynamics

5. Solvation
a. Brief comparison of different solvation methods
b. Periodic boundary conditions

6. Calculation of Thermodynamics Parameters
a. Difficulties with thermodynamics calculations
b. Free energy perturbation method

7. Structure-Based Drug Design
a. Predicting protein-biomolecule structures
b. The search problem
c. Virtual screening
d. Conformational flexibility

The coursework requires some experience in programming. If you do not
have this experience, our course 'Introduction to software development
in Java'
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6250.html) would
be a suitable preparation.

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"Hands-On" Workshop on Computational Biophysics, July 6-10 & August 10-14, 2009, Champaign, IL

2009-01-28T08:45:57Z

"Hands-On" Workshop on Computational Biophysics

http://www.ks.uiuc.edu/Training/Workshop/Champaign09J/
http://www.ks.uiuc.edu/Training/Workshop/Champaign09A/

Application Deadline: May 3, 2009

The Theoretical and Computational Biophysics Group, NIH Resource for
Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the
University of Illinois at Urbana-Champaign (www.uiuc.edu), will
organize a

"'Hands-On' Workshop on Computational Biophysics"

to be held at the following dates and location:

* July 6 to July 10, 2009 at the I Hotel and Conference Center in
Champaign, Illinois
* August 10 to August 14, 2009 at the I Hotel and Conference Center in
Champaign, Illinois

The workshop will explore physical models and computational approaches
used for the simulation of biological systems and the investigation of
their function at an atomic level. The course will be based on case
studies including the properties of membranes and membrane proteins,
mechanisms of molecular motors, trafficking in the living cell through
water and ion channels, and signaling pathways. Relevant physical
concepts, mathematical techniques, and computational methods will be
introduced, including force fields and algorithms used in molecular
modeling, molecular dynamics simulations on parallel computers and
steered molecular dynamics simulations.

The workshop is designed for graduate students and postdoctoral
researchers in computational and/or biophysical fields who seek to
extend their research skills to include computational and theoretical
expertise, as well as other researchers interested in theoretical and
computational biophysics. Theory sessions in the morning will be
followed by hands-on computer labs in the afternoon in which
participants will be able to set up and run simulations.

Applications to the workshop are due by May 3, 2009. Selection and
notification of participants from the application pool will be
completed by May 13, 2009. Those selected to attend must register and
pay a workshop fee by May 23, 2009. The base registration fee is $200
for students, $300 for non-student academics, and $400 for all other
applicants. Double-occupancy housing and all course materials are
included in the fee. All participants are required to bring their own
laptop for use in workshop tutorial sessions. The workshop can neither
fund nor arrange participant travel.

Due to space and equipment constraints, each workshop is limited to 20
participants. For further information, and online application, please
visit the appropriate sites for each date:
* July 6-10 workshop: http://www.ks.uiuc.edu/Training/Workshop/Champaign09J/
* August 10-14 workshop: http://www.ks.uiuc.edu/Training/Workshop/Champaign09A/

Workshop Organizers e-mail contacts by date:
* July 6-10 workshop: workshop+champaign09J@...
* August 10-14 workshop: workshop+champaign09A@...
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Rosetta Academic Training Workshop

2009-01-27T05:00:03Z

Due to public demand, “Rosetta Design Group” is organizing a “Rosetta” software training workshop, aimed for academic groups. The format of the workshop will be a “webinar” - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.*

Nir London | Rosetta Design Group

http://rosettadesigngroup.com/

* If you’re not from an academic group, don’t worry, write us anyway…

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Molecular Modelling and Structure-based Drug Design, March 2009

2008-12-30T14:37:32Z

Molecular Modelling and Structure-based Drug Design, offered by the
University of Leeds, is one of a number of online courses run jointly
with The University of Manchester.

Our distance courses are delivered in a Virtual Learning Environment,
which allows us to extend the classroom into the web. Each course,
which is paced to suit those in full-time employment, runs over 16
teaching weeks.

This course is divided into 7 sections as follows:-

1. Molecular Mechanics
a. The molecular potential energy function
b. The empirical force field
c. Sources of force field data
d. Some examples of important force fields

2. Energy Minimisation
a. First derivative techniques: steepest descent and conjugate gradients
b. Second derivative techniques: Hessian matrix and Newton-Raphson
c. Global optimisation (simulated annealing, Tabu search, genetic
algorithms)

3. Molecular Dynamics and Monte Carlo Simulations
a. Brief introduction to statistical mechanics
b. Molecular dynamics simulations
c. Monte Carlo simulations

4. Conformational Analysis
a. Systematic methods
b. Random search methods
c. Distance geometry
d. Molecular dynamics

5. Solvation
a. Brief comparison of different solvation methods
b. Periodic boundary conditions

6. Calculation of Thermodynamics Parameters
a. Difficulties with thermodynamics calculations
b. Free energy perturbation method

7. Structure-Based Drug Design
a. Predicting protein-biomolecule structures
b. The search problem
c. Virtual screening
d. Conformational flexibility

The coursework requires some experience in programming. If you do not
have this experience, our course 'Introduction to software development
in Java' would be a suitable preparation.

You will find more information on these modules, and on all our other
courses here : http://octette.cs.man.ac.uk/bioinformatics/index.html If
you have any questions, or need advice on the module options, please
contact Heather.Vincent@...

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BCBGC-09 call for papers

2008-11-27T13:17:04Z

BCBGC-09 call for papers The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: • International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) • International Conference on Automation, Robotics and Control Systems (ARCS-09) • International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) • International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) • International Conference on Information Security and Privacy (ISP-09) • International Conference on Recent Advances in Information Technology and Applications (RAITA-09) • International Conference on Software Engineering Theory and Practice (SETP-09) • International Conference on Theory and Applications of Computational Science (TACS-09) • International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) The website http://www.PromoteResearch.org contains more details. Sincerely John Edward Publicity committee

The Macromolecular Modeling Blog

2008-11-27T07:13:02Z

Hi all,

We've started a new blog on all that is related to Macromolecular Modeling
http://rosettadesigngroup.com/blog/

We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears.

please check it out and tell me what you think...
If any of you is interested in writing for the blog I'd be very happy if you contact me.

Cheers,
Nir London.

Rosetta Design Group

http://rosettadesigngroup.com

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e-value

2008-10-18T08:33:51Z

hi all,
i have a set of arabidopsis genes ( approx. 100 ) and want to point
out their orthologs from oryza sativa.Can anyone suggest me the best
method to do this...I was thinking about reciprocal best Basic Local
Alignment Search Tool hits (RBH) but I was confused about the
parameters especially for e-value.Plz sugggest me the optimal e-value
for oorthologs and homologs identification
regards
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Interpolate missing residues in pdb files

2008-07-03T21:56:59Z

Hello,
I am having trouuble with missing residues in pdb files and need to
replace them (i.e. interpolate them) using a program. I think swiss-
pdbviewer and pymol do that. My problem is that I am not very capable
of using those programs and the person whom I asked for help told me
that I have to check for missing residues in pdb file, open swiss-
pdbviewer then add residue at correct place and finally she told me
that I might need to do an energy minimization and I am thinking that
I will definitely do a mistake there. I was wondering if anyone knows
a more automated way to get the missing residues inserted for me
because I am thinking that you can find missing residues in pdb and
and programs can read that info and add these missing residues
themselves automatically.. (but again maybe not..)

Thanks.

Sincerely,
Arif.
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Lattice vs Off-Lattice models

2008-06-09T11:04:49Z

Hi all
I just have a simple question. What is the deffernce(s) between
lattice and off-lattice models in protein folding simulations.

Thank you
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Re: Molmodel Digest, Vol 20, Issue 3

2008-06-02T05:13:58Z

Hi Vladimir ,

The problem with docking inorganic molecules into protein structures is with at atom typing ie Charges to be placed on the atoms..fully charged, partial charges. Most forcefields are either biased to proteins or inorganic molecules and metals. There is no comprehensive forcefield that covers all. You will need to check the forcefield library for the atoms and molecules covered. In general people approximate the charges. Run the expts, see if the molecule is distorted. Rerun expts to overcome after charge modifications for adjusting the distortions.

regards,

Sunil.

On 31/05/2008, molmodel-request@... <molmodel-request@...> wrote:

Send Molmodel mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

  1. Re: inorganic mol. docking (Vladimir Petrov)

----------------------------------------------------------------------

Message: 1
Date: Fri, 30 May 2008 18:16:04 -0400
From: Vladimir Petrov <vpetrov@...>
Subject: [Molecular-modelling] Re: inorganic mol. docking
To: molmodel@...
Message-ID: <g1pub4$iql$1@...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

X-no-archive: yes
sudha.mrig@... wrote:
> I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
> protein molecule.

I guess, you'd have to familiarize yourself with basics of General
Chemistry first, and then decide how to dock ZnSO4 "in organic molecule"
into the protein structure...

------------------------------

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Re: Molmodel Digest, Vol 20, Issue 1

2008-05-19T10:15:05Z

Dear Sudha,

There are no real programs that "docks" inorganic molecules. The best way to handle this is usually you place the molecule in the binding site, set up the forcefields (ie Charges on the molecule), you can add restraints if you know which residues/atoms it co-ordinates to and run MD simulation.

regards,

Sunil.

On 19/05/2008, molmodel-request@... <molmodel-request@...> wrote:

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       molmodel@...

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       http://www.bio.net/biomail/listinfo/molmodel
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       molmodel-request@...

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       molmodel-owner@...

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Molmodel digest..."

Today's Topics:

  1. inorganic mol. docking (sudha.mrig@...)

----------------------------------------------------------------------

Message: 1
Date: Sun, 18 May 2008 09:22:13 -0700 (PDT)
From: sudha.mrig@...
Subject: [Molecular-modelling] inorganic mol. docking
To: molmodel@...
Message-ID:
       <58848cd9-2224-4dc4-b6f0-8124b1637fcf@...>
Content-Type: text/plain; charset=ISO-8859-1

I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
protein molecule. I could not locate any docking software which can
handle in organic molecule.  If anyone can help me in this regard.
Thanks

Sudha

------------------------------

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inorganic mol. docking

2008-05-18T09:22:13Z

I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
protein molecule. I could not locate any docking software which can
handle in organic molecule. If anyone can help me in this regard.
Thanks

Sudha
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TopMatch protein structure alignment and superposition web service

2008-03-25T07:39:25Z

We are pleased to announce the release of TopMatch-web, a public web
service for the alignment and superposition of protein structures and the
instant visualization of structural similiarities.

We believe that TopMatch is an exceptionally effective, accurate, and
enjoyable program for the investigation of protein structure similarities.

For further information and instructive examples see
Sippl & Wiederstein (2008)
A Note on Difficult Structure Alignment Problems.
Bioinformatics 24, pp. 426-427

TopMatch-web is available as a public web service at
http://topmatch.services.came.sbg.ac.at.

Enjoy!

The TopMatch Team
Center of Applied Molecular Engineering
University of Salzburg
Austria

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Structure-Based Drug Design (Conference)

2008-03-14T06:49:37Z

Dear Colleagues,

You can participate at CHI's Structure-Based Drug Design conference on
June 25-27, 2008 at the World Trade Center in Boston, MA.

View full details and register at: www.healthtech.com/sbd/overview.aspx

Presentations by:
AILERON Therapeutics
ARIAD Pharmaceuticals Inc.
AstraZeneca R&D Mölndal
Bristol-Myers Squibb
California Institute of Technology
Centocor Research and Development
Chemical Computing Group Inc.
Elan Pharmaceuticals
Harvard Medical School
Locus Pharmaceuticals
Lundbeck Research (Denmark) Merck Research Laboratories
National Center for Scientifi c Research
(CNRS)
NIH, NIDDK
Novartis
OSI Pharmaceuticals
Pfizer Global Research and Development
Schrodinger, Inc.
SGX Pharmaceuticals
SimBioSys
University of York
Vernalis

Please let me know if you have any questions or if you would like a
PDF brochure emailed to you.

Regards,
Jim Prudhomme
Cambridge Healthtech Institute
jprudhomme@...
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Protein in a membrane

2008-03-10T12:52:25Z

I have one homology model and its in membrane. Can some body tell me how can i sepaate the protein out for a membrane. The whole protein and membrane is in box and filled with the water as well.

I shall be very thankful to you for your kind reply.

with best regards

Rise to the challenge for Sport Relief with Yahoo! for Good
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quiery

2008-01-22T01:19:30Z

Hi There,
I m trying 2 build a theoretical of a protein but unfortunately the
template 4 whole protein is not availabe in PDB so i build 3/4 th part
of protein by compertive modelling while remaining by de novo
method..now I want to ligate the backbone of the both model in order
to generate a complete model.may I do it??if yes then how..plz suggest
a proper method..my mail ID is sanjaysingh765@...
regards
sanjay
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Conference: Structure-Based Design, June 6-8, Boston

2007-05-25T08:20:31Z

Hello:

Conference registrations are still being accepted for CHI's Seventh Annual Structure-Based Design which is scheduled for June 6-8, 2007, World Trade Center, Boston, MA. To register and view the agenda, visit www.healthtech.com/2007/sbd.

With faculty members representing 20+ global pharmaceutical companies, our conference offers more case study findings, cutting-edge science, interactive panel discussions, roundtable discussions, and networking opportunities. On June 6th, participants can attend a pre-conference workshop on Designing Kinase Inhibitors.

At the start of the main conference, Mark Murcko, Ph.D., Vice President & Chief Technology Officer, Vertex Pharmaceuticals, will give the opening keynote address entitled "Hype Versus Reality: How Valuable is Structural Information in Guiding Drug Design?"

Sessions will also include presentations on:
* Experimental Approaches
* Linking Computation, Structures and Chemistry
* Examples of Successful Structural Designs

Please contact me with any questions about this conference.

Sincerely,

James Prudhomme
Cambridge Healthtech Institute
250 First Avenue
Suite 300
Needham, MA 02494
Tel: 781-972-5486
Fax: 781-972-5425

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NOC 3.0 is released

2007-05-16T15:14:04Z

New version NOC-3.0 is released for Windows/Linux/Mac OSX/FreeBSD/Solaris with source code.
Downloading is available at http://noch.sourceforge.net
NOC is:
a easy and fast protein explorer for structure visulization, analysis;
a powerful tool for crystallographic mapping, modeling and refinement;
a efficient viwer for GROMACS/AMBER MD trajectories;

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Enthalpy changes of protein through folding pathway

2007-03-25T06:04:44Z

Hello
I have a very simple question.
Suppose in a protein folding pathway we have two opposite charged
residues seperated by "d" angstrom such that there is a weak
interaction between them. We name it state A, so its enthalpy is Ha.
As protein conformation changes through folding pathway we suppose
"d"
decreases, so interaction between charges become stronger. Now we
name
it State B and its enthalpy as Hb.

My simple question is: is Ha>Hb? or Hb>Ha?

Thanks

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Re: computation time for different molecules

2007-02-20T04:21:01Z

marcus.lundbe@... wrote:

> We have a start already: the larger the molecule, the longer the
> calculation, in general. This rule only results in limited success.
> There is some other feature of the molecule or computation that causes
> some small molecules to take an exorbitant amount of time, and some
> larger molecules are finished very quickly.

Try bionet.biology.computational, people hanging out there may be able
to help.

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computation time for different molecules

2007-02-12T09:17:34Z

Hi,

I'm working on optimizing DOCK6 on a massively parallel computer, and
we're running into a problem with scaling. We'd like to find a way to
estimate the time it takes to dock various ligands in a query. This
information can be used to produce an ordering that allows all the
compute nodes work efficiently without a lot of idle time.

We have a start already: the larger the molecule, the longer the
calculation, in general. This rule only results in limited success.
There is some other feature of the molecule or computation that causes
some small molecules to take an exorbitant amount of time, and some
larger molecules are finished very quickly.

Does anyone know of any similar work being done? Any suggestions or
comments are welcome. (Also, is there another usenet group that might
be a better venue to ask in?)

-Marcus Lundberg

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monte carlo molecular

2007-01-11T12:01:04Z

Dear collegues,
Could somebody indicate me if monte carlo molecular
dynamics program exists? I want to model interaction of respiratory
flow with bronchial tree .
Thanks in advance.
Jane

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[job available] Computational Chemist

2006-12-22T10:47:10Z

Recruiting Computational Chemists and other computational scientists for a company located in New
York City.

In summary, they have a wide variety of needs on their computer science team, from massively
parallel algorithms development to nuts-and-bolts programming. They are interested in seeing
exceptional computer scientists, regardless of specific experience. They are especially interested
in candidates with a background in scientific programming/software development to assist
computational scientists doing chemistry, physics or other simulations.

Here is additional information:

Candidates should have world-class credentials in computational chemistry, biology, or physics, or
in a relevant area of computer science or applied mathematics, and must have unusually strong
research and software engineering skills.

Areas of experience might include the computation of protein-ligand binding free energies, molecular
dynamics and/or Monte Carlo simulations of biomolecular systems, application of statistical
mechanics to biomolecular systems, free energy perturbation methods, and methods for speeding up
evaluation of electrostatic energies -- but specific knowledge of any of these areas is less
critical than exceptional intellectual ability and a demonstrated track record of achievement.

Current areas of interest within the group include the prediction of protein structures and binding
free energies, structure- and ligand-based drug design, de novo ligand design algorithms, and the
development of special-purpose hardware to accelerate computational chemistry simulations.

Both senior- and junior-level members are sought and this company is prepared to offer above-market
compensation to candidates of truly exceptional ability.

Please respond with your CV to resumes@.... Upon receipt, you will receive a
data sheet to complete with additional information.

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Re: protein graft, pdb cleanup

2006-11-28T16:32:04Z

thanks again, that was really helpful, and improved my perl as well.

wkadlo wrote:

> hi, thanks a lot for taking the time to reply with that very helpful
> advice and script.
> i'll give it a go! :-)
>
>
> Raoul Fleckman wrote:
>
> > On 2006-11-27, Raoul Fleckman <raoul.fleckman@...> wrote:
> > > On 2006-11-27, wkadlo <gkowadlo@...> wrote:
> > >
> > > # ---- here alter stuff with the fields (most likely: $asn and $rsn)
> > > #
> > > # for example, if the unchanging part of the protein ends with its
> > > # final residue number ($rsn) equal to 197, then you want to replace
> > > # the $rsn below with "$rsnx++" and initialize it before the above
> > > # "while(<>) {" with "my $rsnx = 198"
> > > # ... and quite similarly for the atom sequence number ($asn)
> > >...
> >
> > bad form replying to myself... but the residue number needs to be set as
> > an increment not on each line as i indicated here, but rather as an
> > offset of whatever the input is: "$rsn += xxx"; where "xxx" will change
> > to old residue sequence number to one beyond the last one seen in the
> > constant part of the protein listing. ...sorry about that. again, good
> > luck.

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Re: protein graft, pdb cleanup

2006-11-27T01:55:57Z

hi, thanks a lot for taking the time to reply with that very helpful
advice and script.
i'll give it a go! :-)

Raoul Fleckman wrote:

> On 2006-11-27, Raoul Fleckman <raoul.fleckman@...> wrote:
> > On 2006-11-27, wkadlo <gkowadlo@...> wrote:
> >
> > # ---- here alter stuff with the fields (most likely: $asn and $rsn)
> > #
> > # for example, if the unchanging part of the protein ends with its
> > # final residue number ($rsn) equal to 197, then you want to replace
> > # the $rsn below with "$rsnx++" and initialize it before the above
> > # "while(<>) {" with "my $rsnx = 198"
> > # ... and quite similarly for the atom sequence number ($asn)
> >...
>
> bad form replying to myself... but the residue number needs to be set as
> an increment not on each line as i indicated here, but rather as an
> offset of whatever the input is: "$rsn += xxx"; where "xxx" will change
> to old residue sequence number to one beyond the last one seen in the
> constant part of the protein listing. ...sorry about that. again, good
> luck.

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Re: protein graft, pdb cleanup

2006-11-26T22:27:32Z

On 2006-11-27, Raoul Fleckman <raoul.fleckman@...> wrote:

> On 2006-11-27, wkadlo <gkowadlo@...> wrote:
>
> # ---- here alter stuff with the fields (most likely: $asn and $rsn)
> #
> # for example, if the unchanging part of the protein ends with its
> # final residue number ($rsn) equal to 197, then you want to replace
> # the $rsn below with "$rsnx++" and initialize it before the above
> # "while(<>) {" with "my $rsnx = 198"
> # ... and quite similarly for the atom sequence number ($asn)
>...

bad form replying to myself... but the residue number needs to be set as
an increment not on each line as i indicated here, but rather as an
offset of whatever the input is: "$rsn += xxx"; where "xxx" will change
to old residue sequence number to one beyond the last one seen in the
constant part of the protein listing. ...sorry about that. again, good
luck.

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Re: protein graft, pdb cleanup

2006-11-26T20:38:21Z

On 2006-11-27, wkadlo <gkowadlo@...> wrote:
> I did the grafting with a hypothetical protein in the program Discovery
> (Accelrys).
> so i have all the 3D coordinates, but the numbering in the file is
> wrong (each fragment has retained the numbering from the original pdb's
> that they came from).

you did "grafting" with "Discovery" which somehow placed the modeled in
bit into a reasonable 3D context (we hope...) and yet the software
having done this failed to simply renumber the atom-sequence-numbers
(and the residue sequence numbers for you)? hmm...

ok..whatever. please keep in mind that the PDB format is old. it has its
roots in punch cards, (please don't ask what that is, if you're too
young to know). therefore, its fields are column number sensitive; and
it is even possible to have numeric fields get large enough so that no
white space is left between fields. therefore, the attached perl script
is designed in an odd (FORTRANish) way to deal with that. if you just
run it on a PDB input without modification, it should just output its
input. that is, you need to figure out what the new atom and residue
sequence numbers ($asn and $rsn, respectively in the script) should be
to continue on after the unchanging sequence and edit the script
accordingly - as per the comments in the script.

here's a second warning: i have observed software that connects residue
N to residue N+1 no matter how many Angstroms might separate them; and
i've seen software that refuses to do so. so if your "i have all the 3D
coordinates" up there isn't quite right, get ready to view some
pretzels.

here's the script appended. it's probably only worth slightly more than
you paid for it; but maybe it'll save you some time. good luck:

#-----------
#!/usr/bin/perl
# 1 2 3 4 5 6 7
#1234567890123456789012345678901234567890123456789012345678901234567890123456
#ATOM 1 CB ASP A 8 -3.48 27.95 19.71 1.00 36.1 A
#ATOM 1439 OW WAT A1259 38.232 42.977 2.328 5.81 7.20 8 10
#ATOM 1 CB ASP 8 -3.220 27.537 20.293 0.00 49.28 6
# put $cid in $segid if $segid is blank or $segid in $cid if $cid is blank
# change nothing if already there
# assumes segid and cid are BOTH one character
# add one to each residue number
# 1- 6 6 $id card id
# 7-11 5 $asn atom sequence number **
#12 1 void
#13-16 4 $anam atom name
#17 1 $ali alternate location indicator
#18-20 3 $rnam residue name
#21 1 void
#22 1 $cid chain identifier
#23-26 4 $rsn residue sequence number **
#27 1 $ci code for insertions (e.g. 66A, 66B)
#28-30 3 void !! is this right ?? there's something up there!!
#31-38 8 $x x coordinate
#39-46 8 $y y coordinate
#47-54 8 $z z coordinate
#55-60 6 $occ occupany
#61-66 6 $bval temperature factor
#67 1 void
#68-70 3 $fn footnote
#71-72 2 void
#73 1 $segid
my $intemp = 'A6 A5 x A4 A A3 x A A4 A x3 A8 A8 A8 A6 A6 x A3 x2 A' ;
#since x generates a zero byte pack must use a different output pattern
my $outemp = 'A6 A5 A A4 A A3 A A A4 A A3 A8 A8 A8 A6 A6 A A3 A2 A A3';
my $K = ' ';
my $K2 = ' ' x 2;
my $K3 = ' ' x 3;
my $sol = $K3;
#a smoother way around this *might* be to make all fields gobble the x before
#it, that is, instead of 'A5 x A4' have 'A5 A5'

while(<>) {
unless (/^ATOM/) {
print;
next;
}
chomp;
my $len = length $_;
if($len < 76) { $_ .= (' ' x (76 - $len)); }

($id,$asn,$anam,$ali,$rnam,$cid,$rsn,$ci,$x,$y,$z,$occ,
$bval,$fn,$segid) = unpack($intemp,$_);

# ---- here alter stuff with the fields (most likely: $asn and $rsn)
#
# for example, if the unchanging part of the protein ends with its
# final residue number ($rsn) equal to 197, then you want to replace
# the $rsn below with "$rsnx++" and initialize it before the above
# "while(<>) {" with "my $rsnx = 198"
# ... and quite similarly for the atom sequence number ($asn)
#
# then you might be able to do something like:
#
# this_script.pl new_attachment.pdb >> copy_of_constant_chain.pdb
#
# ----

my $card = pack($outemp,$id,$asn,$K,$anam,$ali,$rnam,$K,$cid,
$rsn,$ci,$K3,$x,$y,$z,$occ,$bval,$K,$K3,$K2,$segid,$sol);
print $card, "\n" ;
}

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Re: protein graft, pdb cleanup

2006-11-26T17:50:27Z

I did the grafting with a hypothetical protein in the program Discovery
(Accelrys).
so i have all the 3D coordinates, but the numbering in the file is
wrong (each fragment has retained the numbering from the original pdb's
that they came from).

Raoul Fleckman wrote:

> On 2006-11-24, wkadlo <gkowadlo@...> wrote:
> >
> > i have grafted a cap of a protein onto another uncapped protein, and
> > now the pdb file is not consistent.
> >
> > i am about to write a perl script to fix up the numbering and remove
> > the redundant terminus.
> >
> > are there already tools to do such a thing?
>
> there might be such a script available, but that would depend greatly
> what you mean by "grafted". it's not clear if you did that grafting
> at the petrie-dish or the in-silico level. and if it is small change,
> (oh, let's say less than 25 residues), it might be easier, and even
> less error-prone to just perform that edit once in an editor.
>
> if you didn't perform this graft at the petrie-dish level (followed by
> a new structural data set), how do you know the new xyz coordinates?

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Re: protein graft, pdb cleanup

2006-11-24T09:54:23Z

On 2006-11-24, wkadlo <gkowadlo@...> wrote:
>
> i have grafted a cap of a protein onto another uncapped protein, and
> now the pdb file is not consistent.
>
> i am about to write a perl script to fix up the numbering and remove
> the redundant terminus.
>
> are there already tools to do such a thing?

there might be such a script available, but that would depend greatly
what you mean by "grafted". it's not clear if you did that grafting
at the petrie-dish or the in-silico level. and if it is small change,
(oh, let's say less than 25 residues), it might be easier, and even
less error-prone to just perform that edit once in an editor.

if you didn't perform this graft at the petrie-dish level (followed by
a new structural data set), how do you know the new xyz coordinates?
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protein graft, pdb cleanup

2006-11-23T21:30:24Z

i have grafted a cap of a protein onto another uncapped protein, and
now the pdb file is not consistent.

i am about to write a perl script to fix up the numbering and remove
the redundant terminus.

are there already tools to do such a thing?

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Re: Database for protein folded structures

2006-11-15T18:12:59Z

hi sushilee

Have you tried a boolean metasearch like, for example, this one?

http://www.etools.ch/searchSubmit.do?query=database+%28folded+OR+folding+OR+fold%29+%28structures+OR+structure%29+of+%28proteins+OR+protein%29+%28halfway+OR+partial+OR+partially+OR+particularly+OR+particulate+OR+partly+OR+partway+OR+part-way+OR+%28in+part%29%29&logic=AND&timeout=8000&country=web&language=all

I had a eye on it, but i didn't find something yet. Anyway, in my humble opinion your are a bit brief. Maybe a database like SIMAP can help you?
SIMAP is a public database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes.

http://mips.gsf.de/simap/

Andreas

On Wed, 15 Nov 2006 14:27:47 -0800
Sushilee Ranganathan <s_ranganathan@...> wrote:

> I am currently searching for a database that has the partly folded
> structures of proteins (of course, the most important intermediate
> structures) with coordinates, for a friend. I entered this mailing
> list intending to follow up on a message sent out in 1995, when a
> similar question was posted. Could anybody help me out on this?
>
> sushilee
>
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