MUD transcript: 14-06-00
Protein Tertiary Structure II
Course room(s): PPS
14:55:14 ClareS connects.
ClareS PPS HTTP 0s 0s
14:59:18 RamananS connects.
ClareS PPS HTTP 4m 4s 4m 4s
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14:59:54 RamananS says "Hello Clare"
14:59:55 ClareS says "Hi"
15:00:15 ClareS says "I think we should wait a few minutes before starting... see who else comes"
15:00:22 ClareS says "I hope that's OK"
15:01:50 RamananS says (to ClareS) "i hope some one turns up or I will be busted for not reading the course material for terti8ary str.2"
15:02:48 RamananS says (to ClareS) "I am leaving my job from tommrow to enjoy the summer and more importantly to folow the course (catch up really0"
15:07:19 ClareS says "I am most impressed -- will you be going back in the autumn when the weather gets worse again?"
15:07:58 ClareS says "can we start at 16:10 even if no-one else turns up?"
15:08:52 RamananS says (to ClareS) "Yes.it is the best thing to do.i want to learn some Java as it is making a comeback into web technologies, finally...."
15:09:39 RamananS says (to ClareS) "...that is why I have been crying out for a pproject relaed to programming."
15:10:57 RamananS says (to ClareS) "we can start and finish whenever you want."
15:11:20 PaulW connects.
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15:11:48 ClareS says (to PaulW) "Hi -- you haven't missed anything yet we're just about to start"
15:12:23 RamananS says "hello Paul"
15:12:33 PaulW says "O.K. hi"
15:12:34 ClareS says "I don't have the project list here, it will be up by the end of the month I hop"
15:12:42 ClareS says "(hop=hope)"
15:14:17 ClareS says "OK, let's start -- have either of you any particular questions about section 10 of the course material"
15:14:42 RamananS says "can you explain a bit about the exams...."
15:14:58 PaulW says "are projects allocated on a 1st come 1st served basis"
15:16:05 RamananS says "...the exams: will it be testing us exclusively on the course material as has been posted on the pps site"
15:17:19 ClareS says "OK, exams and projects it is (sorry for the slight delay)"
15:17:28 ClareS says "projects first"
15:17:44 ClareS says "we will put the project list up, as I said, hopefully at the end of this month"
15:18:11 ClareS says "the "first come first served" situation doesn't really apply as it's perfectly possible for more than 1 student to do the same project"
15:18:33 ClareS says "we don't allow students in the same institute to do the same project"
15:19:05 ClareS says "you are not allowed to suggest a project but you might be allowed to change the emphasis of one if we agree"
15:20:41 ClareS says "is that clear?"
15:21:11 ClareS says "there will be about 35-40 project titles to choose from"
15:21:46 PaulW says "yes - that sounds fine"
15:22:59 ClareS says "you will be asked to send your choice of project initially to your tutor"
15:23:29 ClareS says "project work starts on 8 August so you will have just over a month to make up your mind on a title"
15:26:05 RamananS says "are our tutors the only help we can get on problems encountered over the projects.or are the projects based on current work at Birkbeck and we get advice from the relevant experts..."
15:27:27 ClareS says "the projects are not based on current work at all if by that you mean unpublished work"
15:28:27 ClareS says "there is also not a particular emphasis on structures and research interests at Birkbeck"
15:28:55 ClareS says "the kind of level we are aiming for is the Web equivalent of a Current Opinion or Trends review"
15:29:22 ClareS says "we have had one or two students who asked us to put them in touch with experts and this has usually worked out fine"
15:33:50 RamananS says "something close to the course material:proteins have structural similarities' - are there any search engines out there/being developed to search on structural classification but not classifying the proteins on the elements/sequence recognised in the macromolecules instead of relying on preclassified information."
15:35:57 ClareS says "sorry I just disappeared into another window"
15:36:32 ClareS says "sorry, I'm not quite sure what you mean..."
15:38:10 RamananS says "....for example some some thing that can search a databases like SCOP for a particular tertiary structue"
15:38:38 RamananS says "..instead of quartenary str."
15:41:38 ClareS says "Scop is a tertiary (not quaternary) structure database, its primary unit of structure is the domain"
15:42:04 ClareS says "you might like to look at FSSP"
15:43:52 ClareS says "and Dali... see http://www.ebi.ac.uk/dali/"
15:45:37 ClareS says "Dali is a server that allows you to compare your own coordinates against every structure in the PDB"
15:45:50 RamananS says "I am sorry I used the wrong terminology.what I am asking for is something that can consider tertiary str. and go on further and look for similar folds and sidechains located in similar positins relative each other."
15:45:59 ClareS says "FSSP is a database made up of an all against all comparison of the PDB using dali"
15:46:08 ClareS says "is that the kind of thing you have in mind?"
15:46:57 ClareS says "it was last updated last week"
15:48:57 ClareS says "it sounds to me as if you are more interested in supersecondary structure"
15:49:24 ClareS says "in looking for structural motifs rather than whole domains -- is that right?"
15:49:52 ClareS says "if so I think someone in Janet Thornton's group has done something relevant -- I'll check it out now"
15:50:32 RamananS says "supersecondary str. is the word.am I correct in saying one could home oin on 'homologous' evolution- I hope I got the word right through this type of search."
15:51:17 ClareS says "if so I think someone in Janet Thornton's group has done something relevant -- I'll check it out now"
15:51:44 ClareS says "yes you did get the word right this time, sorry my browser is reloading very slowly"
15:53:39 ClareS says "there is Procat which you might find interesting - a database of 3d enzyme active site templates"
15:55:02 ClareS says "they describe it as the 3D equivalent of the type of 1D sequence motifs found in Prosite"
15:55:30 ClareS says "see http://www.biochem.ucl.ac.uk/bsm/PROCAT/PROCAT.html"
15:56:01 ClareS says "but the problem is, of course that there are lots of interesting protein structural motifs that are not enzyme active site"
15:56:09 ClareS says "zinc fingers, for example"
15:56:39 ClareS says (to RamananS) "is this the kind of resource you have been thinking of?"
15:58:13 RamananS says "yes.Additionally the combination of these database should do the job I guess"
15:59:32 RamananS says "How does the ProCat end up giving out data exclusively related to known enzyme activity"
15:59:35 ClareS says "yes you can always get much more out of the databases if you combine them"
16:00:03 RamananS says "How does the ProCat end up giving out data exclusively related to known enzyme activity"
16:01:27 ClareS says "Try looking through one of the examples -- the enzymes are categorised by EC number"
16:02:16 ClareS says "the Ser-His-Asp catalytic triad in trypsin is a good example: E.C.22.214.171.124"
16:02:38 ClareS says "there are links to many different types of information"
16:02:57 ClareS says "I don't know why that EC number appears linked up, it certainly doesn't go anywhere"
16:03:08 ClareS says "sorry"
16:03:54 RamananS says "Great, the template page answers most of what i started to inquire about.Thanx"
16:05:07 RamananS says "I mean the Procat enzyme template http://www.biochem.ucl.ac.uk/bsm/PROCAT/templates.html#ec2>"
16:06:18 ClareS says "it is a pity that I don't think that there are any equivalent resources for non-catalytic structural motifs"
16:09:16 RamananS says "I am sure soon there will be a whole new improved and thus easy approach to 3D computing and things will be as we desire."
16:10:33 RamananS says "The exams : Are they exclusive to the course material as phas been posted on the PPS site/"
16:12:46 ClareS says "ah, yes, I'm sorry you asked that question earlier & I forgot to answer it"
16:13:24 ClareS says "I think the best statement of the position is to say that you can pass well knowing nothing but the course material..."
16:13:56 ClareS says "... but that a few extra marks might be available for relevant information from elsewhere in the literature"
16:14:18 ClareS says "that is the same as with all univ. exams at graduate level, I'm sure"
16:15:03 RamananS says "Thank you"
16:17:19 ClareS says "I'd like to close the meeting soon.. do either of you have any more points you'd like to raise quickly?"
16:17:57 RamananS says "I have to go too.Nothing from me."
16:18:18 ClareS says "Paul?"
16:19:18 ClareS looks round expectantly
16:19:56 PaulW says "no - that was intersesting - I think im ready to leave-thanks"
16:20:34 RamananS says "Bye"
16:20:58 PaulW says "cheers"
16:21:42 PaulW disconnects.
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16:21:53 ClareS says "thanks for contributing to an interesting discussion even tho' there were so few of you"
16:22:01 ClareS says "bye"
16:22:05 ClareS waves and leaves
16:22:11 ClareS disconnects.