Re: [ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
As this is a ccp4 bb we should mention the jsPISA server which is at http://www.ccp4.ac.uk/pisa/ This is a very nice implementation of the PISA approach. Another approach is to use the Chimera clash finding approach http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html But this defaults to atom to atom contacts which means you have to prune it down with a script for picking residues. Also does not know about H-bond angles Cheers Martyn Cambridge Original message From : bar...@fmp-berlin.de Date : 18/03/2015 - 14:18 (GMTST) To : CCP4BB@JISCMAIL.AC.UK Subject : [ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex Hi, I just checked the PIC sever tim suggested. very nice indeed. If you only want to map different interfaces and the amino acids involved in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I used it extensively to find out whether a certain set of crystal contacs leads to a certain crystal packing. best, matthias Tim tim.schu...@rub.de 11.03.15 18.25 Uhr Hi, Molprobity is also a nice software to do this kind of analysis - if you use it as implemented in phenix you also get good visualization in coot. I also asked the pymol community to create an implementation for pymol, but I did not follow if somebody took that up. Also this 'protein interactions calculation' server is very neat: http://pic.mbu.iisc.ernet.in/ /Tim On 10/03/15 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Hi all, I should mention 2D-GraLab which is a nice program (you must register to download it) to display in 2D and analyze (a little bit as LigPlot) interactions between two chains within a structure. I have verified the data outputs for several interacting partners using a different program. I can conclude the data is exact and correct up to the second decimal. Enjoy! Nadir Mrabet -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry Ngere - INSERM UMR 954 University of Lorraine, Nancy School of Sciences and Technology School of Medicine 9, Avenue de la Foret de Haye, CS 50184 54500 Vandoeuvre-les-Nancy (France) Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet at univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately. On 10/03/2015 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry Ngere - INSERM UMR 954 University of Lorraine, Nancy School of Sciences and Technology School of Medicine 9, Avenue de la Foret de Haye, CS 50184 54500 Vandoeuvre-les-Nancy (France) Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabet at univ-lorraine.fr Cell.: +33 (0)6.11.35.69.09 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail, or any action taken (or not taken) in reliance on it, is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
[ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Hi, I just checked the PIC sever tim suggested. very nice indeed. If you only want to map different interfaces and the amino acids involved in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I used it extensively to find out whether a certain set of crystal contacs leads to a certain crystal packing. best, matthias Tim tim.schu...@rub.de 11.03.15 18.25 Uhr Hi, Molprobity is also a nice software to do this kind of analysis - if you use it as implemented in phenix you also get good visualization in coot. I also asked the pymol community to create an implementation for pymol, but I did not follow if somebody took that up. Also this 'protein interactions calculation' server is very neat: http://pic.mbu.iisc.ernet.in/ /Tim On 10/03/15 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Thank you all for your valuable suggestions. They have really worked well for me :) Regards, Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
As I'm sure you've also found, it's not simple to find one [easily accessible] program that examines and reports every type of interaction that might be of interest to you. So I'm sending in a reference to another web-based tool that I've found complementary to PISA and the others mentioned here. In particular, it calculates features like the gap volume, number of segments, and the secondary structure-type that dominates between two chains. The tool is called 2P2I Inspector, and can be found here http://2p2idb.cnrs-mrs.fr/2p2i_inspector.html along with other tools and databases that might also interest you. Wishing you well, Emily Arturo Ph.D. program in Biochemistry, Drexel Univ College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA On Wed, Mar 11, 2015 at 1:24 PM, Tim tim.schu...@rub.de wrote: Hi, Molprobity is also a nice software to do this kind of analysis - if you use it as implemented in phenix you also get good visualization in coot. I also asked the pymol community to create an implementation for pymol, but I did not follow if somebody took that up. Also this 'protein interactions calculation' server is very neat: http://pic.mbu.iisc.ernet.in/ /Tim On 10/03/15 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Hi, Molprobity is also a nice software to do this kind of analysis - if you use it as implemented in phenix you also get good visualization in coot. I also asked the pymol community to create an implementation for pymol, but I did not follow if somebody took that up. Also this 'protein interactions calculation' server is very neat: http://pic.mbu.iisc.ernet.in/ /Tim On 10/03/15 11:25, Debasish Kumar Ghosh wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Dear Debasish, Unless I have misunderstood your query this is very much on-topic and sounds a lot like the sort of thing PISA is designed to give you. See http://www.ccp4.ac.uk/html/pisa.html Cheers -- David On 10 March 2015 at 10:25, Debasish Kumar Ghosh dkgh...@cdfd.org.in wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Dear Debasish,For GUI try Pymol, Chimera, CCP4MG.Also try CCP4-CONTACT not an GUI, but you get all possible interactions between two chains.best wishes S.M.Jaimohan, Ph.D On Tuesday, 10 March 2015 3:58 PM, Debasish Kumar Ghosh dkgh...@cdfd.org.in wrote: Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Hi, PDBsum (http://www.ebi.ac.uk/pdbsum/) can also analyze and make a summary of interactions between partners of a protein-protein complex. Just submit your pdb by clicking the 'generate' option from the left menu on the main page. Best, Gulcin Gulten, Ph.D. On Tue, Mar 10, 2015 at 11:57 AM, gert gerrit.vri...@radboudumc.nl wrote: Dear Debasish, The WHAT IF software can do some things for you. As you probably don't want to install a thirty year old package just for some inter-chain contacts, I added a server for you to the WHAT IF servers that are available at http://swift.cmbi.ru.nl/ look under contacts, it is the bottom server on that page. Greetings Gert Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. -- Post-Doctoral Research Associate Texas AM University Dept. of Biochemistry and Biophysics Interdisciplinary Life Sciences Building 301 Old Main Drive, Lab 2138 College Station, Texas 77843
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Dear Debasish, The WHAT IF software can do some things for you. As you probably don't want to install a thirty year old package just for some inter-chain contacts, I added a server for you to the WHAT IF servers that are available at http://swift.cmbi.ru.nl/ look under contacts, it is the bottom server on that page. Greetings Gert Dear All, Apologies for this little off-topic inquiry. I want to closely visualize the interacting residues in an multimeric protein complex to understand the nature of interactions. Is there any good software to give this information with good clarity. Any suggestion is highly appreciated. Thanks, Best !!! Debasish Kumar Ghosh Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.
