From owner-chemistry@ccl.net Thu Feb 4 08:58:01 2010 From: "Iain Moal Iain.Moal**cancer.org.uk" To: CCL Subject: CCL: Papers using PCA to compare MD conformations to crystal structures? Message-Id: <-41179-100204075757-8948-Z5aO9c0AjjmDEDWTgx5RBw===server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CAA591.0258B287" Date: Thu, 4 Feb 2010 11:55:56 -0000 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal###cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAA591.0258B287 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Ian, The book 'Normal Mode Analysis: Theory and Applications to Biological and = Chemical Systems' covers material comparing thermal B-factors, diversity o= f NMR ensembes, atomic fluctuations in MD, MD PCA, full normal mode analys= is and elastic network NMA, as well as lots of references to the primary l= iterature. It is a good starting point. Iain Moal -----Original Message----- > From: owner-chemistry+iain.moal=3D=3Dcancer.org.uk]^[ccl.net on behalf of Ia= n Craig ianrcraig * gmail.com Sent: Wed 03/02/2010 14:49 To: Iain Moal Subject: CCL: Papers using PCA to compare MD conformations to crystal stru= ctures? =20 Sent to CCL by: "Ian Craig" [ianrcraig[*]gmail.com] Dear All, I am looking for papers in which Principal Component Analysis (or similar)= is used to compare the protein conformations visited by an MD trajectory = to a set of crystal (or NMR) structures. I imagine this must have been done in this past to characterize the extent= of conformational sampling accomplished by MD simulations. However, I am = having trouble tracking down firm examples. If anything springs to mind (even if it is just a name and a rough estimat= e of the year), I would greatly appreciate it. Regards, Ian. -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20=20This communication is from Cancer Research UK. Our website is at www.cance= rresearchuk.org. We are a charity registered under number 1089464 and a co= mpany limited by guarantee registered in England & Wales under number 4325= 234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. O= ur central telephone number is 020 7242 0200. =20 This communication and any attachments contain information which is confid= ential and may also be privileged. It is for the exclusive use of the in= tended recipient(s). If you are not the intended recipient(s) please note= that any form of disclosure, distribution, copying or use of this communi= cation or the information in it or in any attachments is strictly prohibit= ed and may be unlawful. If you have received this communication in error,= please notify the sender and delete the email and destroy any copies of i= t. =20 E-mail communications cannot be guaranteed to be secure or=20error free, a= s information could be intercepted, corrupted, amended, lost, destroyed, a= rrive late or incomplete, or contain viruses. We do not accept liability = for any such matters or their consequences. Anyone who communicates with = us by e-mail is taken to accept the risks in doing so. ------_=_NextPart_001_01CAA591.0258B287--