Comments on: Structuregate? http://bytesizebio.net/index.php/2009/12/10/structuregate/ The musings and ravings of a computational biologist about science, computers, music and, you know, stuff Wed, 01 Feb 2012 18:43:57 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Iddo http://bytesizebio.net/index.php/2009/12/10/structuregate/comment-page-1/#comment-628 Iddo Fri, 11 Dec 2009 14:57:03 +0000 http://bytesizebio.net/?p=2866#comment-628 Hari: thanks for compiling and archiving that thread, it makes for very enlightening reading material. I was unaware that this has been going on for so long. Hari: thanks for compiling and archiving that thread, it makes for very enlightening reading material. I was unaware that this has been going on for so long.

]]> By: Hari Jayaram http://bytesizebio.net/index.php/2009/12/10/structuregate/comment-page-1/#comment-627 Hari Jayaram Fri, 11 Dec 2009 09:51:12 +0000 http://bytesizebio.net/?p=2866#comment-627 There was a great discussion on the ccp4bb on 08/17/07 about the several flags raised by one of these structures . Makes great reading . I made a PDF and log file archive of it and put it up. http://harijaycrystdata.s3.amazonaws.com/ccp4bb_archive_thread_withlogfiles_08_17_07_2HR0.zip There was a great discussion on the ccp4bb on 08/17/07 about the several flags raised by one of these structures . Makes great reading .
I made a PDF and log file archive of it and put it up.

http://harijaycrystdata.s3.amazonaws.com/ccp4bb_archive_thread_withlogfiles_08_17_07_2HR0.zip

]]> By: rpg http://bytesizebio.net/index.php/2009/12/10/structuregate/comment-page-1/#comment-626 rpg Fri, 11 Dec 2009 08:32:31 +0000 http://bytesizebio.net/?p=2866#comment-626 Ah... I wondered what had become of this. It was quite apparent two years ago that the Murthy data were fabricated, at least to those of us with any structural smarts at all. When people like Randy Read say 'hang on a minute...' you should listen to them. Ah… I wondered what had become of this. It was quite apparent two years ago that the Murthy data were fabricated, at least to those of us with any structural smarts at all. When people like Randy Read say ‘hang on a minute…’ you should listen to them.

]]> By: Iddo http://bytesizebio.net/index.php/2009/12/10/structuregate/comment-page-1/#comment-625 Iddo Thu, 10 Dec 2009 22:01:04 +0000 http://bytesizebio.net/?p=2866#comment-625 A posting Kevin Karplus to the pdb-l (possibly) expanding the list to 1bgx 1ay1 1hef 1heg 1sbg 1hps 1hos. Also, it seems that RosettaHoles which assesses core packing did not like 1bgx (it's in the RosettaHoles paper, linked from Kevin's posting. https://lists.sdsc.edu/pipermail/pdb-l/2009-December/004991.html From the RosettaHoles paper (published online 2-DEC-2008): "Eight of the outliers, (checking for anomalous core packing, IF) (PDB codes 2A01, 1BEF, 1RID, 1Y8E, 1BGX, 1G44, 2QID, 1G40) are from the Murthy group." A posting Kevin Karplus to the pdb-l (possibly) expanding the list to 1bgx 1ay1 1hef 1heg 1sbg 1hps 1hos. Also, it seems that RosettaHoles which assesses core packing did not like 1bgx (it’s in the RosettaHoles paper, linked from Kevin’s posting. https://lists.sdsc.edu/pipermail/pdb-l/2009-December/004991.html

From the RosettaHoles paper (published online 2-DEC-2008): “Eight of the outliers, (checking for anomalous core packing, IF) (PDB codes 2A01, 1BEF, 1RID, 1Y8E, 1BGX, 1G44, 2QID, 1G40) are from the Murthy group.”

]]> By: Steve http://bytesizebio.net/index.php/2009/12/10/structuregate/comment-page-1/#comment-624 Steve Thu, 10 Dec 2009 21:10:26 +0000 http://bytesizebio.net/?p=2866#comment-624 Wow. Here's a link to an Evernote summary of the structure pages on Pub Med. I think I did all of them: http://www.evernote.com/pub/skoch3/retractedmurthystructures Wow. Here’s a link to an Evernote summary of the structure pages on Pub Med. I think I did all of them: http://www.evernote.com/pub/skoch3/retractedmurthystructures

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