Subject: CCL summary, residue exposure to solvent"

From: <[email-masked]>
Date: Mon, 24 Apr 1995 13:06:01 +0100

From Paul Heelis
North East 
Wales Institute
UK
Recently I posted the following request for help on analyzing solvent exposure
of residues in proteins.
Thanks to all who replied. Here's a summary of the replies

The original posting  
> Does anyone know of a program that can analyse a Brookhaven PDB file and
determine the degree of exposure of a particular residue to the surrounding
solvent and/or measure the effective dielectric constant of its environment.

***********************************************************

From:	SMTP%"[email-masked]"
To:	heelisp
CC:	
Subj:	Re:  CCL:PDB files, residue solvent exposure

Hi, Paul.

The first part can be done with HyperChem and the QSAR Properties module of
ChemPlus.  One would select each residue, one at a time, and import the complete
structure into the module.  The solvent-accessible area is calculated only for
the selected part.  The process would be automated by an Excel macro or a Visual
Basic program.

Regards,
Joel

------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked] 

Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
***********************************************************

From:	SMTP%"[email-masked]"
To:	heelisp
CC:	
Subj:	Re: CCL:PDB files, residue solvent exposure

Paul,
  The upcoming 6.2 release of Sybyl from Tripos includes a new module called
ProTable for the analysis of protein structures.  In addition to numerous
other quantities, ProTable displays the relative solvent accessibility of   each
residue in a protein structure.  It uses the latest version of SAVOL   from Bob
Pearlman and colleagues at the University of Texas, Austin to   compute the
solvent accessibile surface areas for each atom.

  Let me know if you'd like more information.

David Mosenkis  ([email-masked])Tripos, Inc.

***********************************************************
From:	SMTP%"[email-masked]"
To:	heelisp <[email-masked]>
CC:	
Subj:	Re: CCL:PDB files, residue solvent exposure

Hi Paul,

There is a program called whatif around.

we use it alot here.It is free to Academia

you can get it from 

Gert Vriend at EMBL

It is an alround great program that does lots 

and lots of different things.

I can not remember his email but i reckon you

should be able to find him pretty easily .

***********************************************************

From:	SMTP%"[email-masked]"
To:	[email-masked]
CC:	
Subj:	Re: PDB files, residue solvent exposure

Hi Paul,

 The authors are Habsch and Sander.  the
ref. is Biopolymers vol 22 (1983) pp 2577-2637. The paper says DSSP will be
avail. from PDB, but I think we wrote directly to Sander.  Sander's e-mail
address is

   [email-masked]

see ya,
Don

***********************************************************

From:	SMTP%"[email-masked]"
To:	[email-masked]
CC:	
Subj:	Re: CCL:PDB files, residue solvent exposure 

Dear Paul,

A Sybyl module called ProTable is to be released this summer with version6.2 of
Sybyl. ProTable, besides having the functionality of calculatingresidue solvent
exposures, also provides a number of different descriptorsfor the residues in a
protein. The solvent accessibility calculation isbased on SAVOL, a program from
Prof. Robert Pearlman and collegues atTexas, Austin. It is very efficient and
accurate.

Sincerely,

Akbar NayeemBiopolymer Scientist, Tripos Inc.

***********************************************************Subj:	Re: CCL:PDB
files, residue solvent exposure

Hi again,

His e-mail address is [email-masked]

He is not around for a while but you

can still give him a try. He is in Brazil or some such

place.

Paul
================== RFC 822 Headers ==================
***********************************************************
From:	SMTP%"[email-masked]"
To:	[email-masked]
CC:	
Subj:	CCL:PDB files, residue solvent exposure

I guess you have received somethng usefull by now.
All (?) the major Molecular mechanics packages does this.

I use the algorithm by Legrand & Merz (JCC 1993) and could probably makeyou a
quick hack if you do not find anything else. (at the moment the 
routines are incorporated in a way too big program). Unfortunatelyit is in
fortran, so you'd need a fortran compiler.

arne

***********************************************************
From:	SMTP%"[email-masked]"
To:	heelisp
CC:	
Subj:	Re: DSSP

Dear Paul Heelis,

DSSP is sent via e-mail as a C source code that can be compile on any system
(having a C compiler).

Information for the compilation are sent together with the program.

Antoine de Daruvar