Re: [ccp4bb] CASP ROLL needs your structures!
Hi, The definition of new fold at the PDB depends on how it is categorised in SCOP version 1.75, which was released in June 2009. Once the SCOP database is updated again, we'll see how many new folds were really represented by PDB entries deposited in the last few years. Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 20 Jan 2013, at 07:05, Ethan Merritt wrote: On Saturday, 19 January 2013, Luecke, Hartmut wrote: In recent CASPs, there has been a shortage of new folds (according to PDB exactly zero new folds deposited since 2009) and membrane protein targets. I have been wondering about that. It is true that the PDB has not listed any new folds since 2009, but that hasn't stopped people from publishing new structures and claiming they are new folds. Is this because there is no single recognized criterion for new in these cases? Or possibly the PDB hasn't updated their statistics since 2009? E.g. from the 1st page of Google Scholar hits for protein structure new fold 2RSXR Arai, S Fukui, N Kobayashi, J Sekiguchi - JBC 2012 Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold 3RX6R Banerjee, S Nath, A Ranjan, S Khamrui, B Pani, R Sen, U Sen - JBC 2012 A search of the Protein Data Bank using the DALI server (19) and PDBeFold (20) did not produce any significant match with the Psu structure designating it to be a new fold 2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011 Structure and genetic analysis of the arterivirus nonstructural protein 7α Ethan Merritt The lack of such targets makes it problematic to reliably quantify the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
[ccp4bb] CASP ROLL needs your structures!
CASP* ROLL# *Critical Assessment of Structure Prediction #not a new sushi item In recent CASPs, there has been a shortage of new folds (according to PDB exactly zero new folds deposited since 2009) and membrane protein targets. The lack of such targets makes it problematic to reliably quantify the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
Re: [ccp4bb] CASP ROLL needs your structures!
On Saturday, 19 January 2013, Luecke, Hartmut wrote: In recent CASPs, there has been a shortage of new folds (according to PDB exactly zero new folds deposited since 2009) and membrane protein targets. I have been wondering about that. It is true that the PDB has not listed any new folds since 2009, but that hasn't stopped people from publishing new structures and claiming they are new folds. Is this because there is no single recognized criterion for new in these cases? Or possibly the PDB hasn't updated their statistics since 2009? E.g. from the 1st page of Google Scholar hits for protein structure new fold 2RSXR Arai, S Fukui, N Kobayashi, J Sekiguchi - JBC 2012 Solution Structure of IseA, an Inhibitor Protein of dl-Endopeptidases from Bacillus subtilis, Reveals a Novel Fold 3RX6R Banerjee, S Nath, A Ranjan, S Khamrui, B Pani, R Sen, U Sen - JBC 2012 A search of the Protein Data Bank using the DALI server (19) and PDBeFold (20) did not produce any significant match with the Psu structure designating it to be a new fold 2L8K Ioannis Manolaridis, ..., Eric J. Snijder - J. Virology 2011 Structure and genetic analysis of the arterivirus nonstructural protein 7α Ethan Merritt The lack of such targets makes it problematic to reliably quantify the state of the art in the area of protein structure prediction. To remedy this situation, CASP organizers have recently launched a new project called CASP ROLL (http://predictioncenter.org/casprol), where amino acids sequences of challenging targets are released throughout the year when structure solution is imminent. CASP specifically needs sequences of low-homology membrane targets that are about to be solved or have been solved but not released by PDB or elsewhere yet. It is important that structural information about the targets has not been publicly exposed (including things like coordinates, images, papers, conference abstracts) until after the prediction window for a given target has been closed. Each target will be available for prediction for a period of three to four weeks; in some cases a longer hold (up to 8 weeks) may be requested to allow the same target to be re-used for additional modeling experiments. So if you have anything suitable - please let CASP know. As you saw from the information above, your targets need not be fully refined structures. And if you need to make public a target's structure before the CASP window closes, simply contact CASP. We would rather lose a few targets than not have any at all! A good perspective for solving the structure in a few months is a good enough assurance for CASP. The submission mechanism is really simple. You can submit a target using the CASP Target Submission Form (http://predictioncenter.org/casprol/targets_submission.cgi), by sending email to c...@predictioncenter.org, or by marking your PDB deposition as CASP target in PDB's ADIT system (this way PDB will automatically put your target on hold for CASP for 8 weeks). Submission details can be found at http://predictioncenter.org/casprol/targets_submission.cgi Thanks and hoping for lots of targets. Hudel, UC Irvine This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
