Molecular Modeling and Drug Design
  • About us
  • Research
  • Publications
  • Members
  • Webservers
  • Calendar
  • Blog
  • Benchmarks
  • ALLODD
  • Image Gallery
  • Publicity
  • Talks

Drug Discovery: Key Concepts in identifying drug leads

4/14/2014

1 Comment

 
Picture
 How do you decide which leads to follow when developing new drugs? Join  Dr. Tudor Oprea and Dr. Christopher Lipinski as they discuss the Rule of Five, how drug-likeness is a deceiving concept and how lessons from the past may guide the present. Tune in and ask your questions during Part 3 of our Drug Discovery Series.

Watch this live webinar from the American Chemical Society on Thursday, April 24,  2014 @ 2pm ET  

This webinar is also available on the following dates:

Apr 24, 2014 2:00 PM - 3:00 PM EDT
May 29, 2014 2:00 PM - 3:00 PM EDT
Jun 26, 2014 2:00 PM - 3:00 PM EDT
Jul 31, 2014 2:00 PM - 3:00 PM EDT
Sep 25, 2014 2:00 PM - 3:00 PM EDT
Oct 30, 2014 2:00 PM - 3:00 PM EDT

Live ACS Webinars® are free to the public.



1 Comment

nVidia drivers after Ubuntu 12.10

4/11/2014

0 Comments

 
It seems that Ubuntu left out the headers, so it cannot recompile with the nVidia driver correctly.

This is what worked for me, install headers & dpkg update.
https://bugs.launchpad.net/ubuntu/+s...s/+bug/1068942

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install linux-headers-generic
# only reason to purge is there are several versions, if you know you have different nVidia use that:
sudp apt-get purge nvidia*
sudo apt-get install nvidia-current
sudo dpkg-reconfigure nvidia-current


Bug reports:
https://bugs.launchpad.net/ubuntu/+s...s/+bug/1068341

https://bugs.launchpad.net/fglrx/+bug/1068456
https://bugs.launchpad.net/ubuntu/+s...y/+bug/1068488
https://bugs.launchpad.net/fglrx/+bug/1068661
0 Comments

Crystal structure quality assessment

4/10/2014

0 Comments

 
Validation reports are now available for all X-ray structures!

If you go to ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ you can browse for your favourite crystal structure, and get a report on how good/bad it is. Presumably a good thing to do when creating an initial model.

This info was sent to the CCP-BIOSIM mailing list.

The Worldwide Protein Data Bank (wwPDB) partners are pleased to announce that validation reports for all X-ray crystal structures in the PDB archive are now publicly available. The new validation reports are set to become an indispensable resource for both crystallographers and the consumers of structural data who increasingly need to critically assess and compare PDB entries. The reports implement the recommendations of a large group of community experts on validation and include the results of geometric checks, structure-factor assessment and ligand validation. The reports include results from tried and tested software including MolProbity, Xtriage, Mogul, EDS and various CCP4 programs. They summarise the quality of the structure and highlight specific concerns by considering the coordinates of the model, the diffraction data and the fit between the two. Easily interpretable summary information that compares the quality of a structure with that of other structures in the archive is also provided. Validation reports for all X-ray structures archived in the PDB are accessible from the following FTP sites: * ftp://ftp.wwpdb.org/pub/pdb/validation_reports/ (wwPDB) * ftp://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/ (PDBe) * ftp://ftp.pdbj.org/pub/pdb/validation_reports/ (PDBj) The new X-ray structure validation reports have been provided to depositors as part of the structure-annotation process since August 2013. More recently, a stand-alone wwPDB X-ray structure validation server was launched (http://wwpdb-validation.wwpdb.org/). The server allows crystallographers to check early, intermediate and near-final models on demand and helps identify any potential problems that need addressing prior to structure analysis, publication and deposition.

"The stand-alone validation server will run exactly the same validation tests that have recently been introduced for the annotation of new depositions," says Randy Read of Cambridge University. Read chairs the wwPDB X-ray Validation Task Force (VTF) that has produced detailed recommendations to the wwPDB about how macromolecular crystal structures should be validated [1]. "With the stand-alone server, crystallographers won't have any last-minute surprises when they deposit their structures just before submitting the paper," Read adds. The reports have been developed in the context of a larger initiative, the new wwPDB Deposition and Annotation system (http://wwpdb.org/system_info.html), which was created to unify the annotation tools and practices used across all wwPDB deposition centres and for all common structure-determination methods. About wwPDB wwPDB (http://wwpdb.org) is the international partnership that manages the PDB archive. It consists of: the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; http://rcsb.org) and BioMagResBank (BMRB; http://bmrb.wisc.edu) in the USA, the Protein Data Bank in Europe (PDBe; http://pdbe.org) and the Protein Data Bank Japan (PDBj; http://pdbj.org). Together, the wwPDB partners are committed to ensuring high standards of quality, integrity and consistency of this uniquely important archive and to make it freely available for the benefit of scientists worldwide. [1] Read R. J., Adams P. D., Arendall III W. D., Brünger A. T., Emsley P., Joosten R. P., Kleywegt G. J., Krissinel E. B., Lütteke T., Otwinowski Z., Perrakis A., Richardson J. S., Sheffler W. H., Smith J. L., Tickle I. J., Vriend G., and Zwart P. H. A new generation of crystallographic validation tools for the Protein Data Bank. Structure, 19, 1395-1412, 2011. DOI: 10.1016/j.str.2011.08.006 -- Gary Battle Protein Data Bank in Europe (PDBe) EMBL-EBI http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope --


Zoe


0 Comments

    Alexis, Maria, Dimitra, Ioannis,  Michalis, Danai, Panos, George, Aspa, Zoe

    lab group members!

    Enter your email address:

    Delivered by FeedBurner

    Click to set custom HTML

    Archives

    October 2022
    December 2021
    August 2021
    July 2021
    December 2020
    November 2020
    September 2020
    August 2020
    April 2019
    September 2018
    March 2018
    January 2018
    August 2017
    February 2017
    November 2016
    July 2016
    June 2016
    January 2016
    October 2015
    May 2015
    April 2015
    January 2015
    October 2014
    September 2014
    August 2014
    June 2014
    May 2014
    April 2014
    March 2014
    February 2014
    January 2014
    December 2013
    November 2013
    October 2013
    September 2013
    August 2013
    July 2013
    June 2013
    May 2013
    April 2013
    March 2013
    February 2013
    January 2013
    December 2012
    November 2012
    October 2012
    September 2012
    August 2012
    July 2012
    May 2012
    April 2012
    March 2012
    January 2012
    October 2011

    Categories

    All
    64 Bit
    64-bit
    Academia
    Acrobat Reader
    Acroread
    Binding Sites
    Bioinformatics
    Blogging
    Career
    Chembl
    Chemdraw
    Chemistry
    Cloud Computing
    Cluster
    Compounds
    Computational Biology
    Conferences
    Courses
    Crystal Structures
    Databases
    Desktop
    Desmond
    Docking
    Drug Design
    Drug Discovery
    Education
    Email
    Excel
    Fellowships
    Ffmpeg
    Figures
    File Conversions
    Firefox
    Force Field Parameterization
    Fp7
    Free Storage Space
    Glide
    Gpu
    Grant Writing
    Gromacs
    Hpc
    Industry
    Intermolecular Interactions
    Ip Address
    Iphone
    Iso Image
    Jobs
    Library
    Linux
    Lipids
    Literature
    Maestro
    Management
    MAPS
    Materials
    Matlab
    Md Simulations
    Membrane
    Mobile Apps
    Modeling
    Namd
    Network
    Nobel Prize
    Normal Mode Analysis
    Nvidia
    Nwchem
    Off-target Effects
    Pdb
    Pdf
    Peptides
    Photoshop
    Pictures
    Plots
    Postdocs
    Presentations
    Printing
    Problem After Updates
    Programming
    Protein Preparation
    Protein-protein Interactions
    Protocols
    Publishing
    Python
    References
    Review
    Rosetta
    Scheduling
    Schrodinger
    Scripting
    Sitemap
    Solubility
    Ssh
    Teaching
    Trajectory Analysis
    Ubuntu
    Van Der Waals
    Video
    Virtualbox
    Virtual Machine
    Virtual Screening
    Visualization
    Vmd
    Voice Over Ip
    Webinars
    Website
    Writing
    Xmgrace

    RSS Feed

Powered by Create your own unique website with customizable templates.