Ligand Receptor docking
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera. I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters). I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards, Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
Hi Pratik Shriwas, You have to use your own scientific judgment for questions like this. If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
Thank you! Can you send me some publications list which used Chimera (autodock vina). Is there a link where I can find this? Regards, Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University. ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 3:39:15 PM To: Shriwas, Pratik Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Ligand Receptor docking Hi Pratik Shriwas, You have to use your own scientific judgment for questions like this. If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
Sorry, you will have to do your own literature searching! This address is for help in using Chimera, not general research advice. My statement was based on seeing Autodock Vina mentioned in many research papers over the years, but I don’t have a specific list. You could just search for keywords like “vina” or “autodock vina”. However, people who use Autodock Vina are not necessarily using Chimera or the web service; many people download that software and use it directly. It is developed by a group at Scripps: <http://vina.scripps.edu/index.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 12:51 PM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Thank you!
Can you send me some publications list which used Chimera (autodock vina). Is there a link where I can find this?
Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 3:39:15 PM To: Shriwas, Pratik Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Ligand Receptor docking
Hi Pratik Shriwas, You have to use your own scientific judgment for questions like this. If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, Thank you for your advice. I am grateful that you have let me know about the literature. I am sorry if it was offending for me to ask for papers. I meant that sometimes when companies offer their products, they put a citations list. So, I asked. I am sorry. Regards, Pratik Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 9:01:10 PM To: Shriwas, Pratik Cc: chimera-users Subject: Re: [Chimera-users] Ligand Receptor docking Sorry, you will have to do your own literature searching! This address is for help in using Chimera, not general research advice. My statement was based on seeing Autodock Vina mentioned in many research papers over the years, but I don’t have a specific list. You could just search for keywords like “vina” or “autodock vina”. However, people who use Autodock Vina are not necessarily using Chimera or the web service; many people download that software and use it directly. It is developed by a group at Scripps: <http://vina.scripps.edu/index.html> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 12:51 PM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Thank you!
Can you send me some publications list which used Chimera (autodock vina). Is there a link where I can find this?
Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 3:39:15 PM To: Shriwas, Pratik Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Ligand Receptor docking
Hi Pratik Shriwas, You have to use your own scientific judgment for questions like this. If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Pratik, We have lists of Chimera citations (partial list on our website here) <http://www.rbvi.ucsf.edu/chimera/citations.html> … but as I said before, we are not the developers of Autodock Vina. The docking is not done inside of Chimera. Chimera just sends the structures to the outside web service and waits for the results to come back. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 6:06 PM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi,
Thank you for your advice. I am grateful that you have let me know about the literature. I am sorry if it was offending for me to ask for papers.
I meant that sometimes when companies offer their products, they put a citations list. So, I asked. I am sorry.
Regards, Pratik
Get Outlook for Android
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 9:01:10 PM To: Shriwas, Pratik Cc: chimera-users Subject: Re: [Chimera-users] Ligand Receptor docking
Sorry, you will have to do your own literature searching! This address is for help in using Chimera, not general research advice. My statement was based on seeing Autodock Vina mentioned in many research papers over the years, but I don’t have a specific list. You could just search for keywords like “vina” or “autodock vina”. However, people who use Autodock Vina are not necessarily using Chimera or the web service; many people download that software and use it directly. It is developed by a group at Scripps: <http://vina.scripps.edu/index.html>
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 12:51 PM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Thank you!
Can you send me some publications list which used Chimera (autodock vina). Is there a link where I can find this?
Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 19, 2018 3:39:15 PM To: Shriwas, Pratik Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Ligand Receptor docking
Hi Pratik Shriwas, You have to use your own scientific judgment for questions like this. If you mean that you used the Autodock Vina tool in Chimera, it is just an interface to an Autodock Vina webservice provided by another lab, as described in the Chimera Help: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Many publications use Autodock Vina docking, but this web service does not allow for very much sampling because it is a free service used by lots of people. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 11:31 AM, Shriwas, Pratik <ps774614@ohio.edu> wrote:
Hi, I am trying to use UCSF chimera to study ligand-docking interactions. My protein is GLUT1 (4pyp - PDB) and a small molecule called DRB18 .I have used NIH pubchem browser to generate a smiles string for this compound and used the smiles string to generate a 3D structure in chimera.
I have found that the compound interacts with protein in central cavity and interacts via hydrogen bonds (depending on parameters).
I want to know whether my data is publishable. If docking studies performed using chimera are acceptable. People use softwares like Schrodinger/medusa among others. If you wish to see my work, I can send it in as well via email. Thank you. Regards,
Pratik Shriwas Phd Candidate, Molecular and Cellular Biology program, Edison Biotechnology Institute, Ohio University.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Shriwas, Pratik