autodock.scripps.edu

fivth.com

GrahamJ Medical Media Store

http://www.fivth.com/portfolio2.html

Art Appl To Med. Molecule of the Month. Journal and textbook covers, slides, and other editorial figures will appear here soon. On 3/3/11 I posted this temporary link to a Picassa slideshow that highlights a couple of my recent covers. I've got dozens of others and more descriptions to post once I get some free time (they will date back to 1995.). YouTube Animations: Home of GrahamJ.com's Science Channel. Old fiVth.com portfolio. EPMV temp wiki demo 11/19/2010. AutoFill temp wiki demo 4/25/2011. B is a p...

wiki.csi.cuny.edu

Applications Environment - CUNYHPC

http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment

Using Modules to Run your Applications. Modules, Learning by Example. Example 1, Basic Non-Cray System. Example 2, Less Basic From SALK (Cray System). AMBER (Assisted Model Building with Energy Refinement). Gaussian Scratch File Storage Space. Gaussian PBS Job Submission. Modes of Operation in Mathematica. Selecting Between GUI and Command-Line Mode. Using Mathematica on KARLE. Submitting Batch Jobs to the CUNY ANDY Cluster. Serial Batch Jobs Run with 'qsub' Using a Mathematica Command (Text) File. When ...

mgl.scripps.edu

Projects (as of March in 2016) — Molecular Graphics Lab

http://mgl.scripps.edu/projects

Meso-scale Modeling and Visualization. GO Fight Against Malaria 2012-02-06. Embedded Python Molecular Viewer (ePMV) 2012-02-02. 3D Printed Models and Augmented Reality for Chemists 2011-09-20. World Community Grid Lecture Series - FightAIDS@Home 2010-12-08. Projects (as of March in 2016). Computational methods for docking active site ligands (inhibitors), and for elaboration and refined design of inhibitor lead compounds;. Molecular biology/virology of the FIV system. Rapid automated docking of flexible ...

mgl.scripps.edu

Downloads — Molecular Graphics Lab

http://mgl.scripps.edu/downloads

The AutoDock home page - software for automated docking and scoring of flexible ligands to receptors; can also be used for protein-protein docking. New program for fast receptor-ligand docking and affinity prediction. Python Based Software Development at MGL. Which includes the download for Python packages, MSMS binaries, and a pre-compiled Python Interpreter for Unix. Embedded Python Molecular Viewer. The Molecular Graphics Laboratory. Powered by Plone, the Open Source Content Management System.

whitelab.net

Research

http://www.whitelab.net/page1/page1.html

The White Lab @ DrexelMed. Structural Basis of Ligand-gated Ion Channel Function. The biological actions of serotonin (5-HT) are mediated by at least 14 different receptors in seven different families (5-HT. Unlike the other 5-HT receptors, which are G-protein coupled receptors (GPCR's), the 5-HT. R is a ligand-gated cation channel. The 5-HT. R has been implicated in a number of physiological and pathophysiological processes. 5-HT. R antagonists. 5-HT. R) and type C (GABA. How does agonist binding to a s...

dockingtoolbox.blogspot.com

Docking Toolbox: April 2009

http://dockingtoolbox.blogspot.com/2009_04_01_archive.html

A structural biologist experiments with computational biology. Thursday, 23 April 2009. However I do have some ideas for using the programs to simulate molecular dynamics. Monday, 13 April 2009. As a structural biologist I am used to the excellent ccp4 email list populated by the best crystallographers in the world. It is sometimes rather intimidating to post a question, however you always know that you will get an excellent answer. And then you have the autodock email list. oh dear.

dockingtoolbox.blogspot.com

Docking Toolbox: August 2008

http://dockingtoolbox.blogspot.com/2008_08_01_archive.html

A structural biologist experiments with computational biology. Saturday, 2 August 2008. I have posted a snippet of my methods and results from the chapter of my thesis relating to this work here. In retrospect i should have written up and published these results at the time, however the experiments were done prior to some big publications and we did not want to risk the chances of our Nature papers! Subscribe to: Posts (Atom). Open Babel (file converter). Useful Papers (not by me!

dockingtoolbox.blogspot.com

Docking Toolbox: January 2010

http://dockingtoolbox.blogspot.com/2010_01_01_archive.html

A structural biologist experiments with computational biology. Friday, 8 January 2010. Fragment screening for a new cavity. After about six months or so of having given up on automated docking I have returned with a new biological problem to explore. Subscribe to: Posts (Atom). Fragment screening for a new cavity. Open Babel (file converter). Useful Papers (not by me! 2009 Automated Docking Screens: A Feasibility Study. 2007 Evaluations of Molecular Docking Programs for Virtual Screening.

dockingtoolbox.blogspot.com

Docking Toolbox: Fragment screening for a new cavity

http://dockingtoolbox.blogspot.com/2010/01/fragment-screening-for-new-cavity.html

A structural biologist experiments with computational biology. Friday, 8 January 2010. Fragment screening for a new cavity. After about six months or so of having given up on automated docking I have returned with a new biological problem to explore. Subscribe to: Post Comments (Atom). Fragment screening for a new cavity. Open Babel (file converter). Useful Papers (not by me! 2009 Automated Docking Screens: A Feasibility Study. 2007 Evaluations of Molecular Docking Programs for Virtual Screening.

dockingtoolbox.blogspot.com

Docking Toolbox: March 2009

http://dockingtoolbox.blogspot.com/2009_03_01_archive.html

A structural biologist experiments with computational biology. Monday, 9 March 2009. Have been looking at doing some dockings with a protein containing some calcium atoms. A couple years ago I had problems doing this in Autodock, however after speaking so the guys on the autodocking bulletin board I have found the following:. This then raises the question what the charge on the calcium atom should be? Wouldn't it be far more accurate for the charge calculation to take into account the presence of the cal...