From owner-chemistry@ccl.net Fri Jun 24 02:32:00 2011 From: "Gerard Pujadas gerard.pujadas() gmail.com" To: CCL Subject: CCL: more on "starting point to read/learn docking" Message-Id: <-44973-110624022859-23880-C++lnH8l5qwyPxxOCF/dOQ ~~ server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=000e0cd6e7e676e0a704a66f504b Date: Fri, 24 Jun 2011 08:28:48 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas|-|gmail.com] --000e0cd6e7e676e0a704a66f504b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sherin, I published a large survey of protein-ligand docking programs in Current Pharmaceutical Analysis where I talk about the strenghts/weekness of most popular packages (including eHiTS). It was written also from a perspective of guiding new users in the protein-ligand docking field Here is the abstract of this work: *Protein-ligand Docking: A Review of Recent Advances and Future Perspectives. Current Pharmaceutical Analysis. Volume 4, Number 1, pages 1-19, February 2008 * Montserrat Vaqu=E9, Anna Ard=E9vol, Cinta Blad=E9, M. Josepa Salvad=F3, May= te Blay, Juan Fern=E1ndez-Larrea, Llu=EDs Arola and Gerard Pujadas Understanding the interactions between proteins and ligands is crucial for the pharmaceutical and functional food industries. The experimental structures of these protein/ligand complexes are usually obtained, under highly expert control, by time-consuming techniques such as X-ray crystallography or NMR. These techniques are therefore not suitable for routinely screening the possible interaction between one receptor and thousands of ligands. To overcome this limitation, computational algorithms (i.e. docking algorithms) have been developed that use the individual structures of the receptor and ligand to predict the structure of their complex. The present review, then, summarizes: (a) the fundamentals of the algorithms of the most commontly used docking programmes (with particular emphasis on their strengths and limitations); (b) how the results from different docking algorithms compare (i.e. which software gives the best predictions); and (c) the future perspectives and challenges for dockingtechniques. If you are interested in this paper, please do not hesitate to contact me Best Gerard --000e0cd6e7e676e0a704a66f504b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Sherin,

I published a large survey of protein-ligand docking programs in Current Pharmaceutical Analysis where I talk about the=20 strenghts/weekness of most popular packages (including eHiTS). It was writt= en also from a perspective of guiding new users in the protein-ligand docki= ng field

Here is the abstract of this work:

Protein-ligand Docking: A Review of Recent Advances and Future Perspectives. Current Pharm= aceutical Analysis. Volume 4, Number 1, pages 1-19, February 2008

Montserrat Vaqu=E9, Anna Ard=E9vol, Cinta Blad=E9, M. Josepa Salvad= =F3, Mayte Blay, Juan Fern=E1ndez-Larrea, Llu=EDs Arola<= /span> and Gerard Pujadas

Understanding the interactions between proteins and ligands is crucial for the=20 pharmaceutical and functional food industries. The experimental=20 structures of these protein/ligand complexes are usually obtained, under highly expert control, by time-consuming techniques such as X-ray=20 crystallography or NMR. These techniques are therefore not suitable for=20 routinely screening the possible interaction between one receptor and=20 thousands of ligands. To overcome this limitation, computational=20 algorithms (i.e. docking algorithms) have been=20 developed that use the individual structures of the receptor and ligand=20 to predict the structure of their complex. The present r= eview, then, summarizes: (a) the fundamentals of the algorithms of t= he most commontly used docking programmes (with p= articular emphasis on their strengths and limitations); (b) how the results= from different docking algorithms compare (i.e. = which software gives the best predictions); and (c) the future perspectives= and challenges for docking techniques.

If you are interested in this paper, please do not hesitate to co= ntact me

Best

Gerard
--000e0cd6e7e676e0a704a66f504b-- From owner-chemistry@ccl.net Fri Jun 24 06:51:00 2011 From: "Manoj Rudraraju manojrudraraju**gmail.com" To: CCL Subject: CCL: Help with Scaffold Hunter Message-Id: <-44974-110624064439-29775-IdwwST7Z5mJR9wy+WDCrRQ|a|server.ccl.net> X-Original-From: "Manoj Rudraraju" Date: Fri, 24 Jun 2011 06:44:37 -0400 Sent to CCL by: "Manoj Rudraraju" [manojrudraraju=-=gmail.com] Dear CCL memebers, Does any one have experience with latest version of scaffold hunter. when I run Scaffold Tree Generator I see following messages from the log file. ================================ MurckoScaffold c1ccc2c(c1)CC4NCCc3cccc2c34 org.openscience.cdk.exception.CDKException: Exception while writing MDL file: null java.lang.NullPointerException MurckoScaffold or Molecule could not be inserted into DB java.lang.ClassCastException: java.lang.Integer cannot be cast to java.lang.String org.openscience.cdk.exception.CDKException: Exception while writing MDL file: null ================================ I am ready to provide test files and other extra information. Thanks, Manoj