[ccp4bb] AW: [ccp4bb] solvent exposed
Jef, PISA will give you the size of the protein-substrate interface, which is inversely correlated to the solvent exposed surface. Subtracting the interface surface from the total surface of the substrate will give you an estimate of the solvent exposed surface. Best regards, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jeff Holden Gesendet: Mittwoch, 25. Juni 2014 22:11 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] solvent exposed Experts, I would like to compare the substrate binding site of two homologous proteins. Based on crystal structures it is clear that the substrate binding site of protein A is more solvent exposed then protein B. Is there a way to measure the solvent exposure of the substrate in protein A and B? Or perhaps you have an additional suggestion for making a structural comparison (besides what seems obvious...noting the differences in non-covalent interactions)? Thanks, Jeff
[ccp4bb] GRC/GRS Diffraction Methods
Dear all, I am sorry to send one more post to the already overloaded bb, but please let me remind you for the last time that the deadline for applications for the GRC and the GRS is approaching, and is only three days from now. http://www.grc.org/programs.aspx?id=11654 We are all looking forward to welcome you at Bates College in a month from now, and we do hope for a few more last minute participations: we need all of you to make it as exciting and fun as possible! Best regards, Tassos
Re: [ccp4bb] 3D passive monitor for Mac
I think one of our users recently purchased the LG D2343PBBN, but here's an official list (under monitors and monitor/tv's) : https://www.tridef.com/products/pc-licensed-products hopefully some of those are still available. On Wed, Jun 25, 2014 at 9:03 AM, Shawn Xiong wrote: > Hi: > > Recently my 3D Zalman monitor was burned out. > > All the SBGrid suggested models from Asus, LG as well as Zalmon are all > discontinued. > > I am wondering if anyone out there have recently purchased a passive 3D > monitor for Mac that is compatible with all the software commonly used in > structure building and analysis. (coot, pymol, phenix ect.) > > Thanks > > Shawn >
[ccp4bb] solvent exposed
Experts, I would like to compare the substrate binding site of two homologous proteins. Based on crystal structures it is clear that the substrate binding site of protein A is more solvent exposed then protein B. Is there a way to measure the solvent exposure of the substrate in protein A and B? Or perhaps you have an additional suggestion for making a structural comparison (besides what seems obvious...noting the differences in non-covalent interactions)? Thanks, Jeff
[ccp4bb] Postdoctoral position available: RNA-mediated gene regulation
** Postdoctoral Position in RNA-Mediated Gene Regulation ** The research group of Yunsun Nam at UT Southwestern Medical Center is seeking a postdoctoral scholar. Our laboratory is housed in a newly renovated space at the heart of the Cecil H. and Ida Green Center of University of Texas Southwestern Medical Center. Dallas offers many exciting activities, with affordable living costs and convenient housing options near the medical center campus. For more information, please visit the UT Southwestern website. The overarching goal of our group is to elucidate the mechanistic details of RNA-regulated gene expression, by investigating the structure-function relationship of various protein/nucleic acid complexes. We are particularly interested in the gene regulation pathways relevant to mammalian development and cancer. Postdoctoral fellows will have many opportunities to learn the newest methods in biochemistry and biophysics, in addition to working in an exciting, fast evolving area in the field of biological and biomedical sciences. We use various approaches, including X-ray crystallography, NMR spectroscopy, molecular biology, nucleic acid and protein biochemistry, high throughput sequencing, and eukaryotic cell-based studies. For more information, please refer to the lab website: www.ynamlab.org. Candidates must have a Ph.D. degree and a strong background in biochemistry and/or structural biology. Interested individuals should submit a CV as a single pdf file to: Yunsun.Nam AT UTSouthwestern.edu. *UT Southwestern is an Equal Opportunity/Affirmative Action Employer.
[ccp4bb] 3D passive monitor for Mac
Hi: Recently my 3D Zalman monitor was burned out. All the SBGrid suggested models from Asus, LG as well as Zalmon are all discontinued. I am wondering if anyone out there have recently purchased a passive 3D monitor for Mac that is compatible with all the software commonly used in structure building and analysis. (coot, pymol, phenix ect.) Thanks Shawn
[ccp4bb] PhD position in Structural Biology, University of Sussex
A PhD position is available starting in September 2014 in the group of Erika Mancini at the School of Life Sciences, University of Sussex. The University of Sussex has a strong profile of biomedical research, with particular strengths in cell biology and cancer (including the MRC Genome Damage and Stability Centre), neuroscience, and infection and immunity.The successful candidate will join a multidisciplinary group using structural biology, biochemistry, biophysics and cell biology to characterise complexes involved in chromatin remodeling and the regulation of eukaryotic transcription. More information on our research activities is available at the old lab website: ( http://www.strubi.ox.ac.uk/research/erika-mancini ) Applications are invited from recent graduates or final year undergraduates holding or expecting to gain a first or upper second class honours degree. Ideal candidates have a strong background in biochemistry and molecular or cell biology, but science graduates in general are welcome to apply. Preference will be given to candidate with laboratory experience in at least one or more of the following techniques: cloning and mutagenesis, protein expression and purification, X-ray Crystallography or other Structural Biology method. The project is for 3.5 years from September 2014. The stipend is at the standard research council rate. The studentship is only available to UK nationals and EU students due to fee structure. Formal applications should be made at http://www.sussex.ac.uk/study/pg/applying/. While applying please send a full CV, a statement of interest in the project, academic transcripts and two references. Mention Erika Mancini as the suggested supervisor in the application Application deadline 3rd July 2014. For informal project enquiries email Dr Erika Mancini (er...@strubi.ox.ac.uk). For application enquiries email Dr Deeptima Massey (d.mas...@sussex.ac.uk).
