Re: [ccp4bb] Regarding Patents

You cannot patent the “binding site” because it is found in nature (you did not invent it, you discovered it and patents are only granted for inventions). I think you could patent compounds that bind that site if they are not the exact natural ligands. - Francisco On Fri, Nov 3, 2017 at 9:14 PM

Re: [ccp4bb] Regarding Patents

A related question. If you have a crystal structure and found a novel ligand binding site that can be used to regulate protein activity, could you patent such "binding site"? If not, how to make the best use of such findings? Thanks! Cheng On Sat, Nov 4, 2017 at 12:33 AM, James Phillips

Re: [ccp4bb] Regarding Patents

Realistically, if you live in the US and 5 SCOTUS judges agree you can patent anything. On Fri, Nov 3, 2017 at 09:45 Francisco Tenjo wrote: > Hi. > > A mutated DNA or protein molecule can be patented if the mutations are not > present in nature and they have a technical

Re: [ccp4bb] another unknown density problem

Well - I would stick in waters - they can be very well rdered in certain environments. Anecote: We have spent ages trying to put some interesting compound into a "feature" in maps, untill the crystals finally diffracted to 1.6A and in that map it is very clear there are 4 beautifully shaped

Re: [ccp4bb] another unknown density problem

Dear all, My apology for the confusion!! I did mean the map radius is "truncated" at 5A. Poor choice of words :( Any thoughts on what this density could be are still welcome. Best regards, Abhishek On Fri, Nov 3, 2017 at 9:21 PM, Joern Krausze wrote: > Dear all,

Re: [ccp4bb] another unknown density problem

Dear all, I think Abhishek means that the picture shows 5 A map radius. Best Joern > On 3. Nov 2017, at 18:42, Pavel Afonine wrote: > > If by "it was truncated at 5A for clarity" you really mean you truncated all > low-resolution data from 5A and lower then I am not

Re: [ccp4bb] another unknown density problem

If by "it was truncated at 5A for clarity" you really mean you truncated all low-resolution data from 5A and lower then I am not surprised you see funny densities all over or don't see density where it is expected. Why? Consult a textbook for the answer. All the best, Pavel On Fri, Nov 3, 2017

Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem

If you mean you truncated the low resolution data to 5 angstrom, I wouldn't recommend that. On Fri, Nov 3, 2017 at 12:24 PM, Eleanor Dodson wrote: > That map does not look like a 5A map? > I guess you mean something else.. > Eleanor > > On 3 November 2017 at 11:00,

Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem

That map does not look like a 5A map? I guess you mean something else.. Eleanor On 3 November 2017 at 11:00, wrote: > You are right. In this case, I would put some waters in it, refine and see > if the density gets any clearer. However, since from this perspective

[ccp4bb] software to map surface residues

Hello, is there an existing program that can extract the 3D coordinates of the surface residues of a given protein/PDB file? Thanks so much~~ Kai Buck Institute

[ccp4bb] EMBO Practical Course CEM3DIP 2018: of macromolecular assemblies and cellular tomography

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Re: [ccp4bb] Regarding Patents

Hi. A mutated DNA or protein molecule can be patented if the mutations are not present in nature and they have a technical effect (for example, in the case of antibodies, you could have increased affinity for an antigen if you make the right mutations of the CDRs). Also, the mutations should not

[ccp4bb] AW: Re: [ccp4bb] another unknown density problem

You are right. In this case, I would put some waters in it, refine and see if the density gets any clearer. However, since from this perspective the density is quite far away from the protein, it could be a very disordered PEG, which, even at high resolution, might be impossible to fit. Best,

[ccp4bb] CryoEM postdoctoral position at the Wellcome Centre for Cell Biology, Edinburgh, UK | Corrected weblink

A Wellcome Trust funded postdoctoral position is available in Jeyapraksh (JP) Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of Edinburgh. The JP lab (http://jeyaprakash.ed.ac.uk) aims to understand the structural level mechanistic details of processes regulating

[ccp4bb] CryoEM postdoctoral position at the Wellcome Centre for Cell Biology, Edinburgh, UK

A Wellcome Trust funded postdoctoral position is available in Jeyapraksh (JP) Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of Edinburgh. The JP lab (http://jeyaprakash.ed.ac.uk) aims to understand the structural level mechanistic details of processes regulating

Re: [ccp4bb] Regarding Patents

> Sorry for asking out of context question. Can a mutated DNA or protein > molecule be patented. Yes and no. A molecule as such cannot be patented. But the use of a molecule for a specific purpose can be. There are many patents for small molecule drugs, and also for engineered antibodies,

[ccp4bb] AW: [ccp4bb] another unknown density problem

Dear Abhishek, To me, it looks like an alternative conformation of the peptide chain or maybe even a conformational change with respect to the starting model. The peptide chain does not look too well defined, despite high resolution electron density. Best, Herman Von: CCP4 bulletin board

Re: [ccp4bb] coot shelxl problem

Dear all, A simple work around is to add HOH in coot, copy their coordinates into the *.ins fil and refine shelxl from the command line. I have done it a few time and it seems to refine fine. Best regards, Abhishek On Thu, Nov 2, 2017 at 5:40 PM, wrote: > > I am