Re: [ccp4bb] Improving Homology Models
I used proteinmodelportal.org to generate homology models. It worked well for us. Huiming Sent from my iPhone On Feb 20, 2013, at 12:39 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear Crystallographers, it has been my experience that homology modelling programs get folds pretty well, but sometimes the details are pretty obviously bad, like too-close contacts. One might think that the modelling software would put in a sort of polishing step, but they don't seem to. Is there any way to trick the CCP4 or other software to fix these things, such as by simulated annealing or otherwise, I guess without any weight on the [non-existent] structure factors? Thanks, Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***
[ccp4bb] Off-topic: probing hydrophobic surface with ANS
Hi, Could someone refer me to some papers on using ANS to estimate amount of hydrophobic surface in a protein? I tried the classic way by STEP 1: titrating my protein into 1uM ANS till saturation to get the molar fluorescence activity of ANS, then STEP 2: titrate ANS into protein to get amount of fluorescene at plateau so that I can estimate how much ANS is bound per protein molecule. However, for this protein I am dealing with, I can never get the STEP 1 done because the fluorescence signal never saturates. It keeps going up. Are there other ways of getting around this? Thanks, Huiming Li
[ccp4bb] off topic: fluorescence polarization positive control
Hi all, Sorry for the off topic question. Could someone suggest a positive control for FP assay? I am developing this assay and would like to use it for trouble shooting an instrument. Thanks, Huiming Li
[ccp4bb] anomalous scatterer
Hi All, I am working on a Tb binding protein on which I collected anomalous data at Tb edge of 1.648 A. Each protein is designed to bind one Tb. There are two copies of the protein in an ASU. I have two questions. First, I am only able to see one copy of the protein with Tb bound, and no density on the other copy. Isn't this a bit surprising? Second, there is one additional peak on each monomer at the site where Fe is known to bind, and Fe has an edge of 1.739A. At 1.648A, f' and f'' of Fe is only about 1/5 of Tb. Is it possible Fe also shows some anomalous signal at Tb edge? Thank you, Huiming Li, Ph.D. Immune Disease Institute Children's Hospital Boston Harvard Medical School Boston, MA 02115
[ccp4bb] anomalous scatterer
Hi All, I am working on a Tb binding protein on which I collected anomalous data at Tb edge of 1.648 A. Each protein is designed to bind one Tb. There are two copies of the protein in an ASU. I have two questions. First, I am only able to see one copy of the protein with Tb bound, and no density on the other copy. Isn't this a bit surprising? Second, there is one additional peak on each monomer at the site where Fe is known to bind, and Fe has an edge of 1.739A. At 1.648A, f' and f'' of Fe is only about 1/5 of Tb. Is it possible Fe also shows some anomalous signal at Tb edge? Thank you, Huiming Li, Ph.D. Immune Disease Institute Children's Hospital Boston Harvard Medical School Boston, MA 02115
Re: [ccp4bb] peptide docking
Hi, Try Autodock from Scripps. It worked beautifully for me. The docked peptide explained why initial attempts at crystalizing the peptide/protein complex failed (because of a crystal contact). The crystal structure subsequently confirmed the calculated structure. My peptide is a 6-mer. J Mol Biol. 2004 Oct 1;342(5):1659-74 J Mol Biol. 2007 Jun 22;369(5):1296-306 -- Huiming Li Date: Mon, 11 Jul 2011 17:18:48 -0700 From: aac...@gmail.com Subject: Re: [ccp4bb] peptide docking To: CCP4BB@JISCMAIL.AC.UK Hi Rex, The protein I'm working on has a defined substrate-binding cleft. I have a model for the apo form but not the substrate-bound complex. I'd like to dock a peptide fragment of its binding partner potentailly involved in the interaction (~8 residues ) to this cleft. My question is what are some programs people find reliable for making a sensible model of a peptide ligand with the right stereochemistry. As I don't have much experience with peptide docking, I'd really appreciate people sharing their own experience : ) Thanks. On Mon, Jul 11, 2011 at 11:17 AM, REX PALMER rex.pal...@btinternet.com wrote: Hi I'm sure I could help but need more details of the actual project you are undertaking. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com From: crystal aac...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 9 July 2011, 2:09 Subject: [ccp4bb] peptide docking Hi all, As I'm a newbie in peptide docking, I was wondering what programs/servers people would suggest for generating the peptide PDB (keeping all the proper stereochemistry)? Is it possible to extract a file from the PDB database? All comments will be much appreciated!
