From elham.rastegar from gmail.com Sun Oct 4 10:44:10 2009 From: elham.rastegar from gmail.com (elham rastegari) Date: Sun Oct 4 12:13:25 2009 Subject: [Protein-analysis] plant protein extraction Message-ID: Dear all, I did protein extraction from fruit (Curculigo latifolia) according to the attached protocol. I got the white pellet. but while i left it to air dry briefly, i saw the color of pellet got darker, in some parts, it changed to black. i think while i took the phenol phase, unwanted substances entered.Do you have any idea of the type of the substance that causes this, then the pellet was solubilised with urea, thiourea, chaps. agitated for two hours at 4 degree then no parts of pellet remained and all solubilised. then i centrifuge at 12000g for 10 min, in one tube a white substance and in another one an almost dark substance precipitated. i took the supernatant for bradford protein assay. i would be grateful if you could help me identify these unwanted substances. Regards, Eli From afonsomduarte from gmail.com Mon Oct 5 05:13:13 2009 From: afonsomduarte from gmail.com (Afonso Duarte) Date: Mon Oct 5 12:38:09 2009 Subject: [Protein-analysis] How to compare multiple pdb's according to secondary struc+torsion angles Message-ID: <98a320f10910050313jdfa594ft27fe175fd3e4f7d3@mail.gmail.com> Dear All, I have approximately 40 to 50 pdb structures of homologous proteins that I want to compare. I am interested on plotting the sequence vs (secondary structure/torsion_angles/accessibility/hydrophobicity). I have tried software like VMD and WHATIF to do such plots (or part of them) but I am getting problems when the number of structures compared is getting close to 10... Does anybody knows a software/script/webpage that allows such comparison of such number of pdb ? Thanks in advance Afonso From engelbert_buxbaum from hotmail.com Wed Oct 7 08:25:58 2009 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Wed Oct 7 13:20:56 2009 Subject: [Protein-analysis] Re: How to compare multiple pdb's according to secondary struc+torsion angles References: Message-ID: Am 05.10.2009, 06:13 Uhr, schrieb Afonso Duarte : > Dear All, > > I have approximately 40 to 50 pdb structures of homologous proteins > that I want to compare. > I am interested on plotting the sequence vs (secondary > structure/torsion_angles/accessibility/hydrophobicity). I have tried > software like VMD and WHATIF to do such plots (or part of them) but I > am getting problems when the number of structures compared is getting > close to 10... > Does anybody knows a software/script/webpage that allows such > comparison of such number of pdb ? DeepView (formerly the Swiss PDB viewer, www.expasy.ch/spdbv/) can superimpose structures for optical comparison. It can also save a list of phi/psi values (Save - Ramachandran plot) for each protein as text file. You could then enter these values into a spreadsheet for further analysis, or write your own software to do further evaluation. It may be necessary to align the proteins first with Clustal, so that you compare like with like. From bent from cbs.dtu.dk Wed Oct 7 14:51:08 2009 From: bent from cbs.dtu.dk (Bent Petersen) Date: Wed Oct 7 15:44:53 2009 Subject: [Protein-analysis] Secondary Structure and Surface Accessibility predictions easily made Message-ID: Hi Everyone, I have seen that many people are interested in Secondary Structure predictions, and also interested in the surface of proteins. I therefore want to bring your attention to a paper I have recently published, which has the title: A generic method for assignment of reliability scores applied to solvent accessibility predictions., which is freely available here: http://www.biomedcentral.com/1472-6807/9/51 It describes a new method, which is implemented in our freely available method: NetSurfP: http://www.cbs.dtu.dk/services/NetSurfP/ Basically it predicts the secondary structure of a protein, its surface accessibility and also the reliability of surface accessibility prediction in form of a z-score :-) I hope you will find it useful in your research :-) Best Regards, Bent Petersen, Ph.D Student, M.Sc. Center for Biological Sequence Analysis - CBS Department of Systems Biology, Technical University of Denmark. Bld. 208, DK-2800 Lyngby, Denmark