Subject: anal in AMBER 4.1

From: "Sanja Tomic" <[email-masked]>
Date: Thu, 9 Oct 1997 17:02:03 -0600

We would like to use anal (AMBER 4.1 package): 'find' option for more than 10
atoms (what is normally not allowed in anal). We know which subroutines should
be changed, but do not know how to replace original subprogram with the
modified one (to link it to the other routines in the package )... [it is not
quite straightforward.
Can anybody help us?

Thank you!

Sanja

>From [email-masked] Tue Oct  7 17:55 EDT 1997
Date: Tue, 7 Oct 1997 17:53:34 -0400
From: [email-masked] (William S. Hayes)
To: [email-masked]
Subject: UPDATED CONF NOTICE: Gene Discovery in silico Nov 6-9 1997

	
	GEORGIA TECH INTERNATIONAL CONFERENCE IN BIOINFORMATICS

			GENE DISCOVERY IN SILICO
                         
			  NOVEMBER 6 - 9, 1997

                                ATLANTA

The focus of the conference is on gene identification 
and prediction of protein function using computer methods.

SPONSORS: 

Georgia Tech College of Science
Parker H. Petit Institute for Bioengineering and Bioscience at Georgia Tech
SmithKline Beecham
Gene Pro, Inc.
Glaxo-Wellcome

DATES:

     Early registration ends:
          October 9, 1997 

Conference schedule:

     Registration opens at 6:00pm on Thursday, November 6,
          (with the reception at 8:00pm).
     The program starts 8:00am Friday, November 7 
          and ends at noon Sunday, November 9.

LOCATION:

     The conference will be held at
     Renaissance Atlanta Hotel Downtown  
     located near the center of 1996 Olympic development,
     close to Fox Theatre & Georgia Tech  

AGENDA:

The conference agenda includes plenary talks (50 minutes for each 
talk and discussion) as well as poster session and round table discussion.

WWW page now contain all titles as well as abstracts of the 
majority of the plenary talks.

 http://intron.biology.gatech.edu/~william/conference.html

---------------------
Evening - Nov 6
Reception

Morning - Nov 7
Peer Bork	       	EMBL, Heidelberg & MDC, Berlin, Germany
		Predicting function from sequence
Geoff Barton	       	University of Oxford, Oxford, UK & EBI, Cambridge, UK
		Treading the benchmark tightrope: Making progress
		by measuring the accuracy of sequence analysis algorithms
Jim Fickett	       	SmithKline Beecham, King of Prussia, PA
		Analysis of Transcriptional Regulatory Regions
Michael Zhang	       	Cold Spring Harbor Lab, Long Island, NY
		On A New Strategy of Promoter Recognition

Afternoon - Nov 7
Pavel Pevzner	       	University of Southern California, Los-Angeles, CA
		The Twenty Questions Game with Genes
Steven Salzberg	       	Johns Hopkins University, Baltimore, MD
		Decision Trees and Markov Chains for Eukaryotic Gene Finding
Steven Henikoff	       	Fred Hutchinson Cancer Research Center, Seattle, WA
	Blocks-based methods for detecting homology and inferring function
Stephen Altschul       	NCBI/NIH, Bethesda, MD
		More BLAST for Your Buck

Late afternoon - Nov 7 (17:30 - 19:30)
 Poster Session 

Morning - Nov 8
Soren Brunak	       	Technical University of Denmark, Copenhagen, Denmark
		DNA Structure and Sequence Periodicity in Human Promoters
Sam Karlin	       	Stanford University, Stanford, CA
		Codon biases and gene clusters
Jean-Michel Claverie   	Struct & Genetic Information, CNRS, Marseille, France
		Self-identification of protein coding region in bacterial
		genomes
Mark Borodovsky	       	Georgia Institute of Technology, Atlanta, GA
		Three steps to complete gene identification in a new
		 bacterial genome with GeneMark^3

Afternoon - Nov 8
Philipp Bucher	       	ISREC, Lausanne, Switzerland
		Using generalized profiles for functional annotation
		of genome sequences
Michael Gribskov       	San Diego Supercomputer Center, San Diego, CA
		Pattern Recognition Tools for Protein Sequences
Gary Stormo	       	University of Colorado, Boulder, CO
		Combining various types of evidence to predict
		gene structures
Eugene Koonin	       	NCBI/NIH, Bethesda, MD
		A genomic perspective on protein families

Late afternoon - Nov 8 (17:30- 19:30)
Round table discussion 
- "Annotating genomes 
Rapid first pass annotation of large scale sequences"

Morning  - Nov 9
Terry Gaasterland      	Argonne National Lab & Univ of Chicago, Chicago, IL
		Automated Analysis of Whole Genomes: Experiences and Lessons
Anthony Kerlavage      	The Institute for Genomic Research, Rockville, MD
		Gene Finding and Functional Identification in Prokaryotic
		and Eukaryotic Genomes
Roderic Guigo	       	Inst Municipal d'Investigcio Medica, Barcelona, Spain
		Integrating multiple evidence to predict and annotate
		genes in genomic sequences
Victor Solovyev        	Amgen, Inc., Thousand Oaks, CA & Sanger Centre, UK
		A new version of GeneFinder for analysis of genomic
		DNA with multiple genes

STEERING & PROGRAM COMMITTEE:

Mark Borodovsky, Co-Chair, 	Georgia Tech
Soren Brunak			Technical University of Denmark 
Jim Fickett			SmithKline Beecham 
Eugene Koonin, Co-Chair, 	NCBI/NIH 

GEORGIA TECH ORGANIZING COMMITTEE:

Chair 
	Prof. Mark Borodovsky, School of Biology & Mathematics

Advisory board
	Prof. Leonid Bunimovich, School of Mathematics
	Prof. Shamkant Navathe, College of Computing

Poster session
	Dr. Alex Lukashin, School of Biology, 

Publicity
	William Hayes, School of Biology, 
	[email-masked]

Registration and general events
	Laura Olson, Department of Continuing Education, 
	[email-masked]
	Bonnie Griffin, School of Mathematics
	[email-masked]

        We thank Dr. Sorin Istrail and Dr. Ying Xu for help 
        in compiling the e-mail distribution list. 

POSTER SUBMISSION

     To apply for participation in a poster session, 
     please send the title and one page abstract of your poster, 
     by October 3, to Dr. Alex Lukashin, 
     by e-mail: [email-masked] (preferred method) 
     or by FAX: (404) 894-0519.

     You may send the abstract earlier. The acceptance of the high
     quality poster will be confirmed within five days upon submission.

REGISTRATION

     Registration Fee:

          Early (until October 9) $295, Academic/government - $245
          Late: $345, Academic/government - $295

     The registration fee includes handout materials and meals provided by
     Renaissance hotel chefs for the whole conference time. 

Hotel Reservations:

     This conference will be held at the Renaissance Atlanta Hotel
     Downtown. 

     Call Renaissance Atlanta Hotel 404-881-6000 for reservation with Georgia  
     Tech room rate of $99/night by October 3, 1997. Please mention the 
     Bioinformatics/Georgia Tech conference.

Travel Discounts:

     Delta Air Lines offers special fares to attendees of Georgia Tech
     programs. Certain restrictions may apply. For information and
     reservations, call 1-800-241-6760 and refer to file U0175 (for
     domestic flights only).

To obtain more information & the registration form, visit the WWW page: 		
     http://intron.biology.gatech.edu/~william/conference.html

or contact us by 

e-mail:		[email-masked]

Phone:		(404) 894-2400 

Fax:		(404) 894-8925

>From [email-masked] Fri Oct  3 10:42 EDT 1997
Date: Fri, 03 Oct 1997 15:42:12 +0100
To: [email-masked]
From: Peter Tebbutt <[email-masked]>
Subject: ChemSymphony Lite

Dear CCLers,

Apologies for the repeat mailing but it appears our ChemSymphony DNS entry
is currently non-functional. You can reach ChemSymphony Lite via:

http://www.cherwell.com/chemsymphony

Peter Tebbutt

-----------------------------------------------------------
Peter Tebbutt                 | e-mail:  [email-masked]
Development Support           | Tel:     +44 (0)1865 784812
Cherwell Scientific Publishing| Fax:	+44(0)1865 784801
Oxford OX4 4GA, UK            | http://www.cherwell.com
-----------------------------------------------------------
Check Out ChemSymphony - rated top 1% Java applet by JARS
            http://www.cherwell.com/chemsymphony
-----------------------------------------------------------

>From [email-masked] Mon Oct  6 08:49 EDT 1997
Alternate-Recipient: allowed
Auto-Forwarded: prohibited
Content-Return: allowed
Disclose-Recipients: prohibited
Conversion: allowed
Importance: normal
Priority: normal
Sensitivity: Company-Confidential
Subject: re Ovality
From: "R.A. van Gurp" <[email-masked]>
To: [email-masked]
Date: Mon, 6 Oct 97 14:47:24 +0200

Dear Dr. Shapiro

I am working with the same Ovality definition as described by Bodor et al.
Unfortunately I cannot answer your question but I would like to point out that
in order to obtain a dimensionless ovality parameter (a ratio of two radii !)
Formula 9 in JACS 111:3783 (Bodor et al. , 1989) should be read as 

O= (S/4*pi) / [(3V/4*pi)^2/3] , which also reproduces table II page 3786 of the
same article. 

With kind regards,

Ronald A. van Gurp
Prins Maurits Laboratory TNO
PO Box 45
2680 AA Rijswijk
The Netherlands
Email: [email-masked]

>From [email-masked] Mon Oct  6 09:55 EDT 1997
From: "Balasubramanian SIVKUMAR" <[email-masked]>
To: [email-masked]
Subject: logP program
Date: Mon, 06 Oct 1997 06:55:25 PDT

Dear friends,
    I am looking for a program that calculates logP. Is any body provide
me the softwares. Please.
Thanking you,
B.Sivakumar,
SRF. Chemistry,
Bharathidasan University,
Tiruchirappalli-24.
Tamilnadu. India.
e-mail:[email-masked]

______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com