Re: [ccp4bb] books to go

Hey, Are you giving them away or selling them? ;) Cheers Joana Pereira -- PhD student Lamzin Group EMBL Hamburg ℅ DESY Notkestrasse 85 DE-22603 HAMBURG GERMANY Tel:+49 40 89902-276 On 23 Apr 2014, at 21:33, Skrzypczak-Jankun, Ewa ewa.skrzypczak-jan...@utoledo.edu wrote: Hi, I have

Re: [ccp4bb] secondary structure prediction

, Modeller after HHPred (you can do this using the MPI Bioinformatics toolkit) or RaptorX Structure Prediction. I hope this helps you. Best regards and good luck! Dr. Joana Pereira -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Speman

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

or HHPred. You can also let HMMER or HHPred build these profiles for you by giving your sequence as input and play with the parameters. Best, Dr. Joana Pereira -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Spemannstraße 35 72076 Tübingen

[ccp4bb] Senior Postdoctoral Position on Cryo-EM in the Dep. for Protein Evolution at the MPI for Dev. Biology

Dear CCP4 colleagues,Our department is looking for a senior postdoc with experience on Cryo-EM to provide the department with cutting-edge competence in protein structure determination with this method. The position is suitable to start an independent group and independent publication and grant

[ccp4bb] Off-topic: protein 2d diagrams

Dear CCP4 community, I have seen many papers with detailed protein 2d diagrams like this one: However, I can never find a reference for any tool that can compute such diagrams from a 3D structure. Do you know of any? Many thanks and enjoy the warm weather! Joana — Dr. Joana Pereira

[ccp4bb] [Off-topic] Job offer for a Postdoc position in Macromolecular Modelling and Design (MPI Dev. Biology)

of Protein Evolution at the MPI for Developmental Biology. You can find more details on the attached file :) Best regards, Dr. Joana Pereira Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 5 72076 Tübingen GERMANY

Re: [ccp4bb] validating a homlology model

Dear Careina, Your message is a bit confusing... Which kind of validation are you referring to? Do you want to check the geometrical quality of the backbone and side-chain rotamers, or do you want to evaluate how likely it is that the fold proposed by homology actually represents the fold of

[ccp4bb] Omega angles with molprobity

molprobity tool provides that info. Any idea? Many thanks! Best wishes Joana Pereira -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 5 72076 Tübingen GERMANY

Re: [ccp4bb] Omega angles with molprobity

bbie -Original Message- From: CCP4 bulletin board On Behalf Of Joana Pereira Sent: Friday, September 4, 2020 11:29 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Omega angles with molprobity Dear all, Does anyone know which molprobity tool in ccp4/bin lists the omega angles for each r

Re: [ccp4bb] Omega angles with molprobity

20-8235 > Phone : 510-486-5709 Email : nwmoria...@lbl.gov > Fax : 510-486-5909 Web : CCI.LBL.gov <http://cci.lbl.gov/> > > On Fri, Sep 4, 2020 at 5:35 AM Tim Gruene <mailto:tim.gru...@univie.ac.at>> wrote: > Hi Joana, > > unless you are constrain

Re: [ccp4bb] cavities volume calculations

Hi Nathalie, I think Caver tools can do that: https://caver.cz/index.php?sid=133 Best wishes Joana > On 6. Jul 2020, at 15:39, Nathalie Colloc'h wrote: > > Hi everybody, > > I am aware of programs which compute the volume of cavities and pockets. > >

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

nsically Disordered Protein (IDP)*" Oh yes, that is a super good point and I have been thinking about it too. Maybe one should start throwing some IDPs into CASP too :) There's the CAID experiment but, on its current state, AlphaFold would not be possible to test. Best wishes Joana --- Dr

Re: [ccp4bb] Searching Sequence Motif

search database. I hope that helps :) Best, Joana Dr. Joana Pereira | Postdoctoral fellow | Schwede group, Computational Structural Biology | Biozentrum, University of Basel Klingelbergstr. 61, CH-4056 Basel | Email: joana.pere...@unibas.ch <mailto:joana.pere...@unibas.ch> | www.biozentr