Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
As I'm sure you've also found, it's not simple to find one [easily accessible] program that examines and reports every type of interaction that might be of interest to you. So I'm sending in a reference to another web-based tool that I've found complementary to PISA and the others mentioned here. In particular, it calculates features like the gap volume, number of segments, and the secondary structure-type that dominates between two chains. The tool is called 2P2I Inspector, and can be found here http://2p2idb.cnrs-mrs.fr/2p2i_inspector.html along with other tools and databases that might also interest you. Wishing you well, Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA On Wed, Mar 11, 2015 at 1:24 PM, Tim wrote: > Hi, > Molprobity is also a nice software to do this kind of analysis - if you use > it as implemented in phenix you also get good visualization in coot. > I also asked the pymol community to create an implementation for pymol, but > I did not follow if somebody took that up. > > Also this 'protein interactions calculation' server is very neat: > http://pic.mbu.iisc.ernet.in/ > > /Tim > > > On 10/03/15 11:25, Debasish Kumar Ghosh wrote: >> >> Dear All, >> >> Apologies for this little off-topic inquiry. I want to closely visualize >> the interacting residues in an multimeric protein complex to understand the >> nature of interactions. Is there any good software to give this information >> with good clarity. >> Any suggestion is highly appreciated. >> >> Thanks, >> Best !!! >> >> Debasish Kumar Ghosh >> >> CSIR- Junior Research Fellow (PhD Scholar) >> C/o: Dr. Akash Ranjan >> Computational and Functional Genomics Group >> Centre for DNA Fingerprinting and Diagnostics >> Hyderabad, INDIA >> >> Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com >> Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) >> Lab URL: >> http://www.cdfd.org.in/labpages/computational_functional_genomics.html >> >
[ccp4bb] Postdoctoral Position Available
A postdoctoral position is available immediately in the laboratory of Dr. Matthew Gentry (https://biochemistry.med.uky.edu/users/msge222), in the Department of Molecular & Cellular Biochemistry and Center for Structural Biology in the College of Medicine at University of Kentucky. The successful candidate will carry out an independent project on the mechanisms of Lafora disease and neurodegeneration and/or proteins involved in reversible (de)phosphorylation of plant starch using structural biology and biophysical techniques. The lab has a strong record of high impact papers with multiple recent publications in Molecular Cell, The Plant Cell, and PNAS with funding from both the NIH and NSF. Applicants should have a strong background in molecular biology, protein purification, enzyme assays, and protein crystallization. Experience with x-ray diffraction, x-ray collection, and x-ray crystal structure determination is a plus, but not required. The successful applicant will be a highly motivated individual with good communication skills, interest and experience in biochemistry/structural biology in the arena of cell signaling, will have a proven publication record, and the ability to work independently. The applicant must currently have a Ph.D. in Biochemistry or a related field. Competitive salary will be based on qualifications, and appointment will be for 1 year with renewal on a yearly basis. Email a single PDF containing a CV, 1-2 page summary of past research accomplishments, and contact information for three references to matthew.gen...@uky.edu with the subject heading “postdoc.”
[ccp4bb] CCP4 Scientific Programmer Position at CCP4 Core
Dear All, CCP4 has an opening for Scientific Programmer Position in CCP4 Core, located in Research Complex at Harwell, Rutherford-Appleton Laboratory, in some 17 miles south from Oxford, United Kingdom. Job advert and link for on-line applications follow below in this post. If this does not apply to you, please pass this e-mail on your colleagues and friends who may be interested in this exciting opportunity. Many thanks, Eugene Krissinel. CCP4 Scientific Programmer*STFC - The Science and Technology Facilities Council* Location:DidcotSalary:£28,384 to £29,566 per annum plus excellent benefits Hours:Full TimeContract Type:Contract / Temporary Placed on:12th March 2015 Closes:22nd April 2015Job Ref:IRC180113 *About Us: *The Science and Technology Facilities Council is a world-leading multi-disciplinary science organisation, and our goal is to deliver economic, societal, scientific and international benefits to the UK and its people – and more broadly to the world. CCP4 is a large and well-established project, hosted by STFC, with the aim of developing and maintaining state of the art structure solution and analysis software for protein crystallography. The CCP4 Software Suite is one of the most comprehensive and most widely used in its field. *About The Role: *Applications are invited for a CCP4 Scientific Programmer to work in the core CCP4 team. You will assist CCP4 developer’s teams in RAL, University of York and University of Newcastle in the roll-out of CCP4i2, CCP4’s new graphical front end, to end users with subsequent activities on its further development, improvement and increasing functionality. *This is a complex activity, which will include, but is not limited to, the following tasks:* - Develop and maintain the CCP4 release branch related to CCP4i2 and the corresponding development environment. This includes the maintenance of BZR repositories; accommodation of all relevant modifications and additions to the Suite; builds, tests and dynamic updates required for CCP4i2 development and releases - Learn CCP4i2 structure and code for being able to optimise and adopt it as necessary, and introduce new features - Work in close collaboration with CCP4 developers in both UK and overseas on various aspects of CCP4i2 development You will work closely with other members of the core team and there is frequent contact with collaborating scientists, code developers and users. The CCP4 team contribute to several major development projects, and you may be involved in these as appropriate. *About You**You will have the following:* - Degree in numerate science subject or computer science - Good communication skills in English, verbal and written - Experience of software development in both Python and C++ - Ability to analyse and solve problems independently - Ability to collaborate with colleagues at remote sites Knowledge of protein crystallography, as well as practical experience of both unix-based and Windows operating systems, is beneficial but not essential, as all relevant training and introduction will be provided. Candidates with good aesthetic taste for GUI design are particularly welcome. *Benefits: *An excellent index linked pension scheme, 30 days leave allowance and flexi-time are offered. Full details of offered benefits can be found on STFC’s careers pages https://www.stfc.ac.uk/1895.aspx *How to apply: *Applications are handled by UK SBS; to apply please visit our job board at http://www.topcareer.jobs/Vacancy/irc180113_5225.aspx and submit your CV and cover letter. If you are unable to apply online please contact us by telephone on 01793 867000. For an informal discussion about this role please contact: Dr Eugene Krissinel at eugene.krissi...@stfc.ac.uk
