[ccp4bb] Program or server to predict Kd from complex structure
Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei
Re: [ccp4bb] Program or server to predict Kd from complex structure
Hi, PISA have something like this, I think, or at least deltaG estimate. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Wei Liu [we...@me.com] Sent: Thursday, April 18, 2013 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Program or server to predict Kd from complex structure Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei
Re: [ccp4bb] Program or server to predict Kd from complex structure
Hi, As far as I understand the DeltaG given by PISA is kind of a stability measure of the complex, not its binding DeltaG. It is also based on a small part of the terms that contribute to a binding energy. I may be wrong about that, but in any case, predicting a KD from a single structure is something highly risky. The first thing you are leaving out is entropy, which may be the most important term. You can estimate it from normal modes analysis, but you would need to first minimize the energy of the structure. Molecular dynamics (MD) people use a method called MM-PBSA where they try to predict KDs from a number (hundreds or more) of structures extracted from an MD simulation. The method is more or less established, but the results are more meaningful in the context of comparisons than for the prediction of absolute binding energies. If you are only interested in some of the components of the binding energies, like electrostatic and apolar binding and polar/apolar solvation terms, you could use something like APBS (http://www.poissonboltzmann.org/apbs/) Cheers, Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia Le 18/04/13 11:34, Boaz Shaanan a écrit : Hi, PISA have something like this, I think, or at least deltaG estimate. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Wei Liu [we...@me.com] Sent: Thursday, April 18, 2013 11:39 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Program or server to predict Kd from complex structure Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei
Re: [ccp4bb] Program or server to predict Kd from complex structure
For the low cost of $10 USD, this should be about as reliable :) http://www.amazon.com/Mattel-30188-Magic-8-Ball/dp/B1ZWV7 Not trying to be a curmudgeon, but this is a really hard problem! Steve -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wei Liu Sent: Thursday, April 18, 2013 4:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Program or server to predict Kd from complex structure Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Program or server to predict Kd from complex structure
Don't believe such program/server does exist. Notice that you are asking for something that *can* predict Kd. One can *try* making such predictions and they may even be routinely in the ballpark, assuming that you are satisfied with being routinely off by, say, an order of magnitude. One can easily predict general trends. For example, larger buried apolar surface will generally result in lower Kd. As for individual Kd prediction accuracy, that's another story. It's unknown to me what your goal is, but if you are trying to replace experimental Kd determination with a magic program, please don't. Cheers, Ed. Original message From: Wei Liu we...@me.com Date: 04/18/2013 4:39 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Program or server to predict Kd from complex structure Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei
Re: [ccp4bb] Program or server to predict Kd from complex structure
Hi Wei, I'm unsure if this will help, as i've never used it myself, but a former colleague in France is working on such a server? http://2p2idb.cnrs-mrs.fr/ But as everyone else has stated, only use this in comparison to some hard physical data. Cheers, Mat From: Ed. Pozharski epozh...@umaryland.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 18 April 2013, 8:46 Subject: Re: [ccp4bb] Program or server to predict Kd from complex structure Don't believe such program/server does exist. Notice that you are asking for something that *can* predict Kd. One can *try* making such predictions and they may even be routinely in the ballpark, assuming that you are satisfied with being routinely off by, say, an order of magnitude. One can easily predict general trends. For example, larger buried apolar surface will generally result in lower Kd. As for individual Kd prediction accuracy, that's another story. It's unknown to me what your goal is, but if you are trying to replace experimental Kd determination with a magic program, please don't. Cheers, Ed. Original message From: Wei Liu we...@me.com Date: 04/18/2013 4:39 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Program or server to predict Kd from complex structure Dear all, Does anyone know a program or web server that can predict Kd value between two proteins from a solved complex structure? Regards Wei
