From owner-chemistry@ccl.net Fri Jan 23 05:43:01 2009 From: "Pau Farr s pfarras\a/icmab.es" To: CCL Subject: CCL:G: trueno server Message-Id: <-38488-090123051625-7389-B9R6nsCuVzj2liH1g5PmyQ_+_server.ccl.net> X-Original-From: "Pau Farr s" Date: Fri, 23 Jan 2009 05:16:14 -0500 Sent to CCL by: "Pau Farr s" [pfarras(0)icmab.es] Hi, I'm trying to use the cubegen and formchk utilities of Gaussian in trueno server from CSIC. The problem is that I cannot load the module related to Gaussian because I have no idea which one it is. Anybody can help me please? Thank you! From owner-chemistry@ccl.net Fri Jan 23 05:59:00 2009 From: "Siamkhanthang Neihsial sktn06:_:gmail.com" To: CCL Subject: CCL:G: Computational Chemistry Software Message-Id: <-38489-090123055539-15453-6l8OPyqulokhrBtE7fwGfg . server.ccl.net> X-Original-From: "Siamkhanthang Neihsial" Date: Fri, 23 Jan 2009 05:55:35 -0500 Sent to CCL by: "Siamkhanthang Neihsial" [sktn06]|[gmail.com] Dear CCLers, I have been working in the apllication of computational chemistry software(MOPAC, PC GAMESS, GAUSSIANS)since sometimes. Now, i am inclined to the thought of how a programmer of those or others scintific software needs to do or know. Here is my query 1. How many programming languages(C,C++,Fortran, java...) a programmer need to know before he writes a software ? And how did he made use of these languages in software development? 2. Does he needs to know some extra courses like "Advanced course in Software development" in addition to the above programming languages? regards, Siamkhanthang Neihsial, PhD Research Scholar, Dept. of Chemistry, Nprth-Eastern Hill University, Shillong,India sktn06 . gmail.com From owner-chemistry@ccl.net Fri Jan 23 08:49:01 2009 From: "Sebastian Radestock sebastian],[radestock.net" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38490-090123041052-1573-pWuOQY6hNzcEJYDSBVGa7g/./server.ccl.net> X-Original-From: "Sebastian Radestock" Date: Fri, 23 Jan 2009 04:10:48 -0500 Sent to CCL by: "Sebastian Radestock" [sebastian,radestock.net] Dear all, I'm looking for a software that allows for introducing single amino acid mutations into a protein structure. A subsequent local minimization or optimization should also be possible. Any hint would be appreciated. Kind regards, Sebastian Radestock. -- Dipl. Bioinf. Sebastian Radestock Computational Pharmaceutical Chemistry Christian-Albrechts-Universitt zu Kiel Telefon: 0431 880 1120 URL: http://www.radestock.net Mail: sebastian]_[radestock.net From owner-chemistry@ccl.net Fri Jan 23 09:25:00 2009 From: "Sebastian Radestock sebastian!=!radestock.net" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38491-090123035727-563-jT+zEsHP98YYYvZUGGhmRw++server.ccl.net> X-Original-From: Sebastian Radestock Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 23 Jan 2009 09:57:15 +0100 MIME-Version: 1.0 Sent to CCL by: Sebastian Radestock [sebastian^radestock.net] Dear all, I'm looking for a software that allows for introducing single amino acid mutations into a protein structure. A subsequent local minimization or optimization should also be possible. Any hint would be appreciated. Kind regards, Sebastian Radestock. --=20 Dipl. Bioinf. Sebastian Radestock Computational Pharmaceutical Chemistry Christian-Albrechts-Universit=E4t zu Kiel Telefon: 0431 880 1120 URL: http://www.radestock.net Mail: sebastian---radestock.net From owner-chemistry@ccl.net Fri Jan 23 09:58:00 2009 From: "Herbert Fruchtl herbert.fruchtl _ st-andrews.ac.uk" To: CCL Subject: CCL:G: Computational Chemistry Software Message-Id: <-38492-090123081055-6672-Rpi1pL1CBkMw8PLcA2/HJw=-=server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 23 Jan 2009 12:40:21 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl(!)st-andrews.ac.uk] > I have been working in the apllication of computational chemistry software(MOPAC, PC GAMESS, GAUSSIANS)since sometimes. Now, i am inclined to the thought of how a programmer of those or others scintific software needs to do or know. Here is my query > 1. How many programming languages(C,C++,Fortran, java...) a programmer need to know before he writes a software ? And how did he made use of these languages in software development? Most programs are written in one language. Some of the larger programs use two (Fortran/C, Fortran/C++, Python/C,...), but it quickly becomes a nightmare to port them between platforms and compilers if you have to interface more languages. None of these programs are really written by one person. The criteria for choosing a language are: - What are the contributors good at? Fortran programmers write horrible C++... - Are you planning to use existing building blocks from other programs? - Is performance important? If yes, you're down to Fortran and C (or simple C++ that looks like C). - What will most of the code do? If it's system access, I/O etc., C/C++ are good. For linear algebra and multidimensional arrays, Fortran is unbeatable. Web applications and graphics? Use Python or Java. > 2. Does he needs to know some extra courses like "Advanced course in Software development" in addition to the above programming languages? > In theory it wouldn't hurt. In practice, it is more important to understand the science, so it's done by chemists and physicists who learnt programming it by doing it, and by making mistakes... But any program larger than 200 lines needs proper specifications, design of interfaces and data structures, etc., which a "Fortran for Chemists" course won't teach you. PLEASE don't use this as yet another excuse for a language war. Herbert -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Jan 23 10:34:01 2009 From: "Michel Petitjean petitjean.chiral .. gmail.com" To: CCL Subject: CCL:G: Computational Chemistry Software Message-Id: <-38493-090123085039-11239-DpuOjxH2pCKBFTqt0Z8frQ:-:server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=000e0cd6a8ac36b735046126957c Date: Fri, 23 Jan 2009 14:44:06 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral::gmail.com] --000e0cd6a8ac36b735046126957c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, That's interesting questions. I began to write scientific softwares when I was a doctoral student, and I found that there was no major difficulty to write programmes on the basis of what I learned (fortran: yes, it was a long time ago). Because I liked programming, I learned some other languages by myself, and I was able to write programmes in these languages without much pain. Only one condition was necessary: to like programming. Then I went five years in a private company selling scientific softwares (Questel). And here, I realized that there is an enormous gap between writing small softwares at the University and writing modules to be incorporated in complex industrial softwares. If the programme you are writing were to be selled rapidly to get money, you would not care to do a good programming: you are paid to work fast so that your company do not spend much money to develop low quality softwares and receive much money after selling the products. But if the modules you are contributing are part of a high quality software to be maintained during many years by the company, you have much more to learn: how to define clearly input, ouput, functionalities, formats, setting modularity, portability, parametrization, documentation, probable evolutions etc. Note that you need also a sufficient knowledge of numerical analysis, operation research, simulation, and more generally all what is related to math programming. Without that, the company would lose incredible amounts of money and probably could not survive. It does not seem to me that this all that is taught at the University (except math programming in some cursus), and most academics recognized for their contributions in computational sciences (not only computational chemistry) are unaware of what really means programming at the advanced level (you have understand that I do not mean using advanced language instructions, which in general must be avoided for portability reasons). Then, the debate about which languages to learn is thus of minor importance: you just need to be able to learn languages and to select the appropriate ones when required. Writing some small routines in two or three usual languages may be informative, and normally, if you know one language, you can easily learn an other one. Actually, most cursus involve C, and the longest life language if fortran (older that most of us), still taught at some places. Even writing a routine solving the second degree equation could be an excellent exercise to differentiate an experienced programmer from an experienced scientist having only a basic knowledge of programming. Unfortunately, the committees who evaluate scientific developpers at the University are themselves unexperienced, and they consider that programming is a low level technical task of little value: proof, their young ten years children are fluent with Word and Windows, so why programming should be difficult for scientists ? If you would like to earn money or you would like to do a beautiful career at the University, you do not need to be an experienced programmer. If you really would like to be an efficient programmer recognized by those who are really competent in that field, you may enjoy to learn advanced programming techniques, but you will more likely get that in a limited number of private companies rather than in the Universities (well, it seems to be the situation in France: opinions from other countries are welcome). Best regards, Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean++cea.fr, petitjean.chiral++gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ---------- Forwarded message ---------- > From: Siamkhanthang Neihsial sktn06:_:gmail.com Date: 2009/1/23 Subject: CCL:G: Computational Chemistry Software To: "Petitjean, Michel " Sent to CCL by: "Siamkhanthang Neihsial" [sktn06]|[gmail.com] Dear CCLers, I have been working in the apllication of computational chemistry software(MOPAC, PC GAMESS, GAUSSIANS)since sometimes. Now, i am inclined to the thought of how a programmer of those or others scintific software needs to do or know. Here is my query 1. How many programming languages(C,C++,Fortran, java...) a programmer need to know before he writes a software ? And how did he made use of these languages in software development? 2. Does he needs to know some extra courses like "Advanced course in Software development" in addition to the above programming languages? regards, Siamkhanthang Neihsial, PhD Research Scholar, Dept. of Chemistry, Nprth-Eastern Hill University, Shillong,India sktn06*|*gmail.com --000e0cd6a8ac36b735046126957c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
That's interesting questions. I began to write scientific softwa= res when I was a doctoral student, and I found that there was no major diff= iculty to write programmes on the basis of what I learned (fortran: yes, it= was a long time ago). Because I liked programming, I learned some other la= nguages by myself, and I was able to write programmes in these languages wi= thout much pain. Only one condition was necessary: to like programming.
Then I went five years in a private company selling scientific softwares (Q= uestel). And here, I realized that there is an enormous gap between writing= small softwares at the University and writing modules to be incorporated i= n complex industrial softwares.
If the programme you are writing were to be selled rapidly to get money, yo= u would not care to do a good programming: you are paid to work fast so tha= t your company do not spend much money to develop low quality softwares and= receive much money after selling the products.
But if the modules you are contributing are part of a high quality software= to be maintained during many years by the company, you have much more to l= earn: how to define clearly input, ouput, functionalities, formats, setting= modularity, portability, parametrization, documentation, probable evolutio= ns etc. Note that you need also a sufficient knowledge of numerical analysi= s, operation research, simulation, and more generally all what is related t= o math programming.
Without that, the company would lose incredible amounts of money and probab= ly could not survive.
It does not seem to me that this all that is taugh= t at the University (except math programming in some cursus), and most acad= emics recognized for their contributions in computational sciences (not onl= y computational chemistry) are unaware of what really means programming at = the advanced level (you have understand that I do not mean using advanced l= anguage instructions, which in general must be avoided for portability reas= ons).
Then, the debate about which languages to learn is thus of minor importance: you just need to be able to learn languages and to select the appropriate ones when required. Writing some small routines in two or three usual languages may be informative,
and normally, if you know one language, you can easily learn an other one. Actually, most cursus involve C, and the longest life language if fortran (older that most of us), still taught at some places.
Even writi= ng a routine solving the second degree equation could be an excellent exerc= ise to differentiate an experienced programmer from an experienced scientis= t having only a basic knowledge of programming.
Unfortunately, the committees who evaluate scientific developpers at the Un= iversity are themselves unexperienced, and they consider that programming i= s a low level technical task of little value: proof, their young ten years = children are fluent with Word and Windows, so why programming should be dif= ficult for scientists ?
If you would like to earn money or you would like to do a beautiful career = at the University, you do not need to be an experienced programmer.
If y= ou really would like to be an efficient programmer recognized by those who = are really competent in that field, you may enjoy to learn advanced program= ming techniques, but you will more likely get that in a limited number of p= rivate companies
rather than in the Universities (well, it seems to be the situation in Fran= ce: opinions from other countries are welcome).
Best regards,

Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 5= 28,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908 4006 / Fax: = +331 6908 4007
E-mail: michel= .petitjean++cea.fr, petitj= ean.chiral++gmail.com
h= ttp://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

---------- Forwarded message ----------
From: Siamkhanthang Neihsial sktn06:_:gmail.com <owner-chemistry++ccl.net>
Date: 2009/1/23
Subject: CCL:G: Computational Chemistry Software
To: = "Petitjean, Michel " <petitjean.chiral++gmail.com>

Sent to CCL by: "Siamkhanthang  Neihsial" [sktn06]|[gmail.com]
Dear CCLers,
 I have been working in the apllication of computational chemistry so= ftware(MOPAC, PC GAMESS, GAUSSIANS)since sometimes. Now, i am inclined to t= he thought of how a programmer of those  or others scintific software = needs to do or know. Here is my query
1. How many programming languages(C,C++,Fortran, java...) a programmer need= to know before he writes a software ? And how did he made use of these lan= guages in software development?
2. Does he needs to know some extra courses like "Advanced course in S= oftware development" in addition to the above programming languages?
regards,

Siamkhanthang Neihsial,
PhD Research Scholar,
Dept. of Chemistry,
Nprth-Eastern Hill University,
Shillong,India
sktn06*|*gmail.com


--000e0cd6a8ac36b735046126957c-- From owner-chemistry@ccl.net Fri Jan 23 13:22:00 2009 From: "Chupakhin Vladimir chupvl|*|gmail.com" To: CCL Subject: CCL: Toxophores database Message-Id: <-38494-090123131847-12655-TCbATQXp7LPsZYB7ZF7MUg\a/server.ccl.net> X-Original-From: Chupakhin Vladimir Content-Type: multipart/alternative; boundary=0015175ca8663563b804612a6931 Date: Fri, 23 Jan 2009 21:18:08 +0300 MIME-Version: 1.0 Sent to CCL by: Chupakhin Vladimir [chupvl+*+gmail.com] --0015175ca8663563b804612a6931 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL subscribers, I am looking for the database of the toxophores (mutagens, teratogenes, etc) - open or academically avaliable. The only one I have found is Benigni-Bossa rulebase implemented in ToxTree software. Also there is a DEREK software from LHASA that also have rule-based toxophores but it's commercial. Are there anything else except above mentioned? Vladimir Chupakhin, Moscow State University --0015175ca8663563b804612a6931 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL subscribers,
 
I am looking for the database of the toxophores (mutagens, teratogenes= , etc) - open or academically avaliable. The only one I have found is = Benigni-Bossa rulebase implemented in ToxT= ree software. Also there is a DEREK software from LHASA that also have rule= -based toxophores but it's commercial.
 
Are there anything else except above mentioned?
 
 
Vladimir Chupakhin,
Moscow State University
--0015175ca8663563b804612a6931-- From owner-chemistry@ccl.net Fri Jan 23 13:57:00 2009 From: "Elaine Meng meng . cgl.ucsf.edu" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38495-090123121118-2052-hfBV1KiH3E5K9OynkLbKbg|-|server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 23 Jan 2009 12:11:15 -0500 Sent to CCL by: "Elaine Meng" [meng]^[cgl.ucsf.edu] Hi Sebastian, With UCSF Chimera, you can use the "Rotamers" tool (or command "swapaa") to substitute amino acids in proteins. It can help you choose, or choose for you, the rotamer with the fewest steric conflicts. There are a couple of choices of rotamer library, including Dunbrack backbone-dependent. You can also select a zone around that amino acid for minimization with "Minimize Structure" (or "minimize" command). Currently the minimization tool is rather limited, and will not handle structures with certain metal ions. I personally favor the results from swapaa/Rotamers without minimization, if there is a rotamer that does not clash with the rest of the structure. If for noncommercial use, you can just go the Web site and download Chimera (Windows, Mac, Linux): http://www.cgl.ucsf.edu/chimera/index.html More information on those Chimera features: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html Best, Elaine ----- Elaine C. Meng, Ph.D. meng##cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Fri Jan 23 15:26:00 2009 From: "John W Daily john.daily|,|colorado.edu" To: CCL Subject: CCL:G: Computational Chemistry Software Message-Id: <-38496-090123140058-3254-syM2I3ZlDGcdGmdqzELiPQ]_[server.ccl.net> X-Original-From: John W Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 23 Jan 2009 11:28:21 -0700 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: John W Daily [john.daily###colorado.edu] Folks, There is an engineering discipline called "software engineering." (see: http://en.wikipedia.org/wiki/Software_engineering) To quote Wikipedia "Software engineering is the application of a systematic, disciplined, quantifiable approach to the development, operation, and maintenance of software, and the study of these approaches." Naturally, most of us science types tend to ignore such things, although using versioning systems like SVN is a form of software engineering. As to programming languages, I started out using BUFTRAN, the predecessor of fortran, on an IBM 650 that used vacuum tubes and a 4K rotating drum memory the size of a large backyard barbeque. I still write mostly in fortran, although Michel's suggestion to write code snippets in different languages is a good exercise. I have recently written smaller programs in matlab, mathematica, TCL, Igor Pro's scripting language, and bash. John On Jan 23, 2009, at 6:44 AM, Michel Petitjean petitjean.chiral .. gmail.com wrote: > Hi, > That's interesting questions. I began to write scientific softwares > when I was a doctoral student, and I found that there was no major > difficulty to write programmes on the basis of what I learned > (fortran: yes, it was a long time ago). Because I liked programming, > I learned some other languages by myself, and I was able to write > programmes in these languages without much pain. Only one condition > was necessary: to like programming. > Then I went five years in a private company selling scientific > softwares (Questel). And here, I realized that there is an enormous > gap between writing small softwares at the University and writing > modules to be incorporated in complex industrial softwares. > If the programme you are writing were to be selled rapidly to get > money, you would not care to do a good programming: you are paid to > work fast so that your company do not spend much money to develop > low quality softwares and receive much money after selling the > products. > But if the modules you are contributing are part of a high quality > software to be maintained during many years by the company, you have > much more to learn: how to define clearly input, ouput, > functionalities, formats, setting modularity, portability, > parametrization, documentation, probable evolutions etc. Note that > you need also a sufficient knowledge of numerical analysis, > operation research, simulation, and more generally all what is > related to math programming. > Without that, the company would lose incredible amounts of money and > probably could not survive. > It does not seem to me that this all that is taught at the > University (except math programming in some cursus), and most > academics recognized for their contributions in computational > sciences (not only computational chemistry) are unaware of what > really means programming at the advanced level (you have understand > that I do not mean using advanced language instructions, which in > general must be avoided for portability reasons). > Then, the debate about which languages to learn is thus of minor > importance: you just need to be able to learn languages and to > select the appropriate ones when required. Writing some small > routines in two or three usual languages may be informative, > and normally, if you know one language, you can easily learn an > other one. Actually, most cursus involve C, and the longest life > language if fortran (older that most of us), still taught at some > places. > Even writing a routine solving the second degree equation could be > an excellent exercise to differentiate an experienced programmer > from an experienced scientist having only a basic knowledge of > programming. > Unfortunately, the committees who evaluate scientific developpers at > the University are themselves unexperienced, and they consider that > programming is a low level technical task of little value: proof, > their young ten years children are fluent with Word and Windows, so > why programming should be difficult for scientists ? > If you would like to earn money or you would like to do a beautiful > career at the University, you do not need to be an experienced > programmer. > If you really would like to be an efficient programmer recognized by > those who are really competent in that field, you may enjoy to learn > advanced programming techniques, but you will more likely get that > in a limited number of private companies > rather than in the Universities (well, it seems to be the situation > in France: opinions from other countries are welcome). > Best regards, > > Michel Petitjean, > DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, > 91191 Gif-sur-Yvette Cedex, France. > Phone: +331 6908 4006 / Fax: +331 6908 4007 > E-mail: michel.petitjean++cea.fr, petitjean.chiral++gmail.com > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > > ---------- Forwarded message ---------- > From: Siamkhanthang Neihsial sktn06:_:gmail.com +ccl.net> > Date: 2009/1/23 > Subject: CCL:G: Computational Chemistry Software > To: "Petitjean, Michel " > > Sent to CCL by: "Siamkhanthang Neihsial" [sktn06]|[gmail.com] > Dear CCLers, > I have been working in the apllication of computational chemistry > software(MOPAC, PC GAMESS, GAUSSIANS)since sometimes. Now, i am > inclined to the thought of how a programmer of those or others > scintific software needs to do or know. Here is my query > 1. How many programming languages(C,C++,Fortran, java...) a > programmer need to know before he writes a software ? And how did he > made use of these languages in software development? > 2. Does he needs to know some extra courses like "Advanced course in > Software development" in addition to the above programming languages? > > regards, > > Siamkhanthang Neihsial, > PhD Research Scholar, > Dept. of Chemistry, > Nprth-Eastern Hill University, > Shillong,India > sktn06*|*gmail.com > > From owner-chemistry@ccl.net Fri Jan 23 16:02:00 2009 From: "Mathew T. Mizwicki mathew.mizwicki[]ucr.edu" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38497-090123141204-12061-96aC9UJd8ghI8rSrMVBfjg#%#server.ccl.net> X-Original-From: "Mathew T. Mizwicki" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 23 Jan 2009 10:34:57 -0800 MIME-Version: 1.0 Sent to CCL by: "Mathew T. Mizwicki" [mathew.mizwicki::ucr.edu] Sebastian Radestock sebastian!=!radestock.net wrote: > Sent to CCL by: Sebastian Radestock [sebastian^radestock.net] > Dear all, > > I'm looking for a software that allows for introducing single amino acid > mutations into a protein structure. A subsequent local minimization or > optimization should also be possible. > > Any hint would be appreciated. > > Kind regards, > Sebastian Radestock. > > > Sebastian, i use Discovery Studio 2.0; however, i'm sure there is free ware available for this as well, Matt From owner-chemistry@ccl.net Fri Jan 23 16:35:00 2009 From: "Anders Blom anders.blom_._quantumwise.com" To: CCL Subject: CCL: New version of Atomistix ToolKit released by QuantumWise Message-Id: <-38498-090123145259-7106-tU4U4YUR734TGvaTKHH6Ng===server.ccl.net> X-Original-From: "Anders Blom" Date: Fri, 23 Jan 2009 14:52:55 -0500 Sent to CCL by: "Anders Blom" [anders.blom|,|quantumwise.com] As earlier preliminarily announced, the newly started company QuantumWise has assumed all legal rights to continue the development and distribution of the first-principles transport code Atomistix ToolKit (ATK), following the bankruptcy in September of Atomistix. All existing customers contracts with Atomistix will be fully honored for support and rights to upgrades and maintenance. We are also happy to announce the release of ATK 2008.10. Thanks to the latest improvements in the software, this release runs 2-5 times faster than before and now allows for DFT simulations (also transport) of over 1,000 atoms, using as little as 2 Gb for certain parameter choices. Please visit our homepage http://www.quantumwise.com for more information, and to request a free trial license. Anders Blom -- Anders Blom, Ph.D. Sales, Marketing and Support Manager QuantumWise A/S From owner-chemistry@ccl.net Fri Jan 23 17:12:00 2009 From: "Grace Y Tier Grace.Y.Tier .. usa.dupont.com" To: CCL Subject: CCL: Toxophores database Message-Id: <-38499-090123160100-10670-mlWSAm7oafFMWc7zxD40xw^server.ccl.net> X-Original-From: Grace Y Tier Content-Type: multipart/alternative; boundary="=_alternative 006DECD985257547_=" Date: Fri, 23 Jan 2009 15:00:39 -0500 MIME-Version: 1.0 Sent to CCL by: Grace Y Tier [Grace.Y.Tier/a\usa.dupont.com] This is a multipart message in MIME format. --=_alternative 006DECD985257547_= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" MCASE is another expert system that contains toxicophores but this is commercial. The only one that comes to mind that is not commerically available is the OECD Toolbox. Within the Toolbox you will find a number of profiling tools e.g. Verhaar scheme, Protein binding, DNA binding. The DNA binding tool identifies structural features that are indicative of genotoxic action. see http://www.oecd.org/document/23/0,3343,en_2649_34379_33957015_1_1_1_1,00.html#Download_the__QSARs_Application_Toolbox for more details on how to download and install. There is a wealth of training material available for the Toolbox. Much of that is aimed at users who wish to apply the Toolbox for the development and evaluation of chemical categories and read-across. The profiling tools are one means to evaluate the "similarity with respect to a chemical mechanism of action". Grace "Chupakhin Vladimir chupvl|*|gmail.com" Sent by: owner-chemistry+grace.y.tier==usa.dupont.com^^^ccl.net 01/23/2009 02:25 PM Please respond to "CCL Subscribers" To Grace Y Tier/AE/DuPont^^^DuPont cc Subject CCL: Toxophores database Dear CCL subscribers, I am looking for the database of the toxophores (mutagens, teratogenes, etc) - open or academically avaliable. The only one I have found is Benigni-Bossa rulebase implemented in ToxTree software. Also there is a DEREK software from LHASA that also have rule-based toxophores but it's commercial. Are there anything else except above mentioned? Vladimir Chupakhin, Moscow State University This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html --=_alternative 006DECD985257547_= Content-Transfer-Encoding: 7bit Content-Type: text/html; charset="us-ascii"
MCASE is another expert system that contains toxicophores but this is commercial. The only one that comes to mind that is not commerically available is the OECD Toolbox. Within the Toolbox you will find a number of profiling tools e.g. Verhaar scheme, Protein binding, DNA binding. The DNA binding tool identifies structural features that are indicative of genotoxic action.

see http://www.oecd.org/document/23/0,3343,en_2649_34379_33957015_1_1_1_1,00.html#Download_the__QSARs_Application_Toolbox for more details on how to download and install. There is a wealth of training material available for the Toolbox. Much of that is aimed at users who wish to apply the Toolbox for the development and evaluation of chemical categories and read-across. The profiling tools are one means to evaluate the "similarity with respect to a chemical mechanism of action".


Grace




"Chupakhin Vladimir chupvl|*|gmail.com" <owner-chemistry^^^ccl.net>
Sent by: owner-chemistry+grace.y.tier==usa.dupont.com^^^ccl.net

01/23/2009 02:25 PM
Please respond to
"CCL Subscribers" <chemistry^^^ccl.net>
To
Grace Y Tier/AE/DuPont^^^DuPont
cc
Subject
CCL: Toxophores database





Dear CCL subscribers,
 
I am looking for the database of the toxophores (mutagens, teratogenes, etc) - open or academically avaliable. The only one I have found is  Benigni-Bossa rulebase implemented in ToxTree software. Also there is a DEREK software from LHASA that also have rule-based toxophores but it's commercial.
 
Are there anything else except above mentioned?
 
 
Vladimir Chupakhin,
Moscow State University 
This communication is for use by the intended recipient and contains
information that may be Privileged, confidential or copyrighted under
applicable law. If you are not the intended recipient, you are hereby
formally notified that any use, copying or distribution of this e-mail,
in whole or in part, is strictly prohibited. Please notify the sender by
return e-mail and delete this e-mail from your system. Unless explicitly
and conspicuously designated as "E-Contract Intended", this e-mail does
not constitute a contract offer, a contract amendment, or an acceptance
of a contract offer. This e-mail does not constitute a consent to the
use of sender's contact information for direct marketing purposes or for
transfers of data to third parties.

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--=_alternative 006DECD985257547_=-- From owner-chemistry@ccl.net Fri Jan 23 17:47:00 2009 From: "Niels Johan Christensen njc#%#life.ku.dk" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38500-090123163404-17365-RC7buUgoWb+fmXydE5uJ6A^server.ccl.net> X-Original-From: "Niels Johan Christensen" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 23 Jan 2009 20:51:04 +0100 Mime-Version: 1.0 Sent to CCL by: "Niels Johan Christensen" [njc^life.ku.dk] Dear Sebastian, You can use Swiss-PdbViewer to create mutations and subsequently select the best rotamer for the sidechain. More information : http://www.expasy.ch/spdbv/text/mutation.htm As far as I know, Swiss-PdbViewer does not offer the possibility of local geometry-optimization, so you´ll probably have to perform this task with another piece of software. Best, Niels >>> "Sebastian Radestock sebastian],[radestock.net" 01/23/09 10:10 AM >>> Sent to CCL by: "Sebastian Radestock" [sebastian,radestock.net] Dear all, I'm looking for a software that allows for introducing single amino acid mutations into a protein structure. A subsequent local minimization or optimization should also be possible. Any hint would be appreciated. Kind regards, Sebastian Radestock. -- Dipl. Bioinf. Sebastian Radestock Computational Pharmaceutical Chemistry Christian-Albrechts-Universitt zu Kiel Telefon: 0431 880 1120 URL: http://www.radestock.net Mail: sebastian{}radestock.nethttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jan 23 18:46:01 2009 From: "Andrew Orry orry.molsoft**gmail.com" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38501-090123184430-19301-ae/6tO0PX5kVwkFNoljqxg===server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Fri, 23 Jan 2009 15:45:13 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [orry.molsoft-#-gmail.com] ICM-Pro allows you to easily make mutations and optimize (http://www.molsoft.com/icm_pro.html). For an interesting application see: Bordner AJ, Abagyan RA. Proteins. 2004 Nov 1;57(2):400-13.Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations. Thanks, Andy -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Niels Johan Christensen njc#%#life.ku.dk wrote: > Sent to CCL by: "Niels Johan Christensen" [njc^life.ku.dk] > Dear Sebastian, > > You can use Swiss-PdbViewer to create mutations and subsequently select > the best rotamer for the sidechain. > > More information : http://www.expasy.ch/spdbv/text/mutation.htm > > As far as I know, Swiss-PdbViewer does not offer the possibility of > local geometry-optimization, so you´ll probably have to perform this > task with another piece of software. > > Best, > Niels > > > > > >>>> "Sebastian Radestock sebastian],[radestock.net" >>>> > 01/23/09 10:10 AM >>> > > Sent to CCL by: "Sebastian Radestock" [sebastian,radestock.net] > Dear all, > > I'm looking for a software that allows for introducing single amino acid > mutations into a protein structure. A subsequent local minimization or > optimization should also be possible. > > Any hint would be appreciated. > > Kind regards, > Sebastian Radestock. > > >