BioMoo held on the 13th May 1999

ClareS turns the ClareS_recorder on.

ClareS says "welcome - we are here to discuss (mostly) section 9 of the course material - is there anything specific you'd like to talk about?"

AndyS says "9?"

ClareS says "typo - I typed 9 instead of 8. Sorry..."

ClareS blushes (

ClareS says "think not a good start..."

Gmocz [to ClareS] I guess it is about secondary structure rather than molecular forces as the e-mail indicated, but I nay be wrong

ClareS says "yes - secondary structure"

Gmocz [to ClareS] The older PDB files usually listed the TURNs, the newer ones not.What program do you think is best to extract TURNs/

ClareS says "Interesting question..."

ClareS says "I get the impression that there is rather less interest in turns now than there was in the first few decades of protein secondary structure research"
Gmocz Why is that?

ClareS says "I am not sure, but certainly all the fold classification programs use helices, sheets and topology rather than turns"

ClareS says ""do you know the PDBsum database?\"

ClareS says "this gives a summary and a structural analysis of each file in the PDB"

ClareS says "there is a nice toplological plot of each structure which shows the turns well"

Gmocz [to ClareS]
Gmocz but maybe I just want too much. PDBsun is nice

ClareS says "look up something like retinol binding protein - it shows many turns"

ClareS says "so what you are looking for is a *program* for calculating turns rather than just a database that lists them - am I right?"

Gmocz [to ClareS] I just would like to have something with unique identification.The Kabsh&Sander algorithm seems to list more SSE, especially turns than usually given by the crystallographers. Should one use the crystallographers assignments?

ClareS says "Kabsch & Sander does list a number of secondary structure elements of rather dubious value - such as extremely short helices and sheets"

ClareS says "if the crystallographers list turns, I should take it that those are the only turns there are"

Gmocz [to ClareS] That is probably true. But sometime not everyrging is listed, just those which have some interst

ClareS says "the problem with turns is that the definition is not as fixed as for helices & strands"
Gmocz Oh,my bad typing...

ClareS says "and there are a number of different types of turn, so identification is going to be more complex"
Gmocz I guess whatever is listed is more reliable than Kabsh&Sander (Anyway K&S is the standard for PDB How come?

ClareS says "because K&S was the first system for ID'ing secondary structure elements created, I would expect. Anyway it *is* extremely useful - it's just that any assessment using geometric parameters is best backed up using the eye of an experienced structural biologist"

ClareS says "another good site with a detailed listing of turns is PROMOTIF - do you know it?"

ClareS says "this goes into a lot of detail about turn types"

Gmocz [to ClareS] Is a crystallographer's SSE assignment always based on hydrogen bonding, or sometime pure geometry is used only?
Gmocz No, I do not know PROMOTIF. Something I have to check it out now that you called my attention to it

Gmocz [to AndyS] How about you,Andy Do you know PROMOTIF?
(ClareS has disconnected.)
(ClareS has connected.)

ClareS says "sorry - connection problems"

AndyS says "I've never heard of it before now, something that often happens to me in these sessions!"

ClareS says "try for an excellent example of a structure with a lot of turns, listed in detail"

ClareS [to AndyS] don't worry about it - that's what we're here for

AndyS says "I know, I am lucky to be on such a steep learning curve"

ClareS says "and I hadn't realised what a lot of secondary and super-secondary structural info there is here: strands, helices, turns (by type), bulges, hairpins"

ClareS says "I don't know what a "hairpin" is, but it's not the same as a turn!"

ClareS . o O ( and it also lists disulphides primary structure )

Gmocz [to ClareS] In the meantime I made a connection to the site you suggested. It looks very detailed. Certainly, later on I want to check it out more thoroughly

ClareS [to gmocz] do I assume that you're still interested in checking out programs?

ClareS says "maybe we should have pointed to promotif from section 8?"

Gmocz [to ClareS] Well, I myself do not know exactly , yes and no
ClareS . o O ( another one of us.. )

Gmocz [to Geraint] Hello!!
ClareS is wondering if Procheck might be useful

Gmocz [to ClareS] Procheck implements K&S with some extensions. Basically Procheck extentend helices and sheets ti a little bit longer form

ClareS says "Procheck *is* useful - not only for secondary structure analysis"
Gmocz Oh, typing. But I sure you know what I meant

ClareS says "one important disadvantage of Kabsch & Sander - it only goes by geometry, so a bent helix might appear as two helices separated by one or two residues"
Gmocz Sure, Its other applications are much more important

Gmocz [to ClareS] Do you know how does Stride fit into this picture, I mean SSE assignment. It is closer to crystallographers, but I am not sure

ClareS says "do any of you have user names on the UK MRC's Human Genome Mapping Project resource centre machine?"
Gmocz NO

AndyS says "not me"

ClareS says "that is an excellent repository of software for sequence & structure analysis, mostly web based, but you do need to register"

ClareS says "it's free, even for those located outside the UK"

AndyS says "who can register?"

AndyS says "and how"

ClareS says "see"

ClareS says "it's meant for UK academics, but they don't turn anyone away and if you're not in industry you don't pay for anything but GCG"

ClareS says "see e.g. the secondary structure analysis menu:"

AndyS says "thanks, it looks good"

ClareS says "there's a link to STRIDE there"

ClareS says ":will need to go in 10 minutes or so"
ClareS can't type
Gmocz (This is funny. I could access the Registered page without registration...)
Gmocz I am in Predator now.
Gmocz OK, I am back.

ClareS says "are you sure? it only throws you out at the very last minute, when you try to run the software"

ClareS says "to tantalise you and make you register straight away!"
Gmocz It could be. Actually I did not run the program, jist called the page.
Gmocz jist->just

ClareS says "one useful thing is that all the documentation is online"
Gmocz To summarize up then, it is more important to concentrate on the topological aspects than on turns in describing structure. I guess that is your main point
Geraint materializes out of thin air.

ClareS says "yes, I would think that that is a fair summary"

ClareS [to Geraint] welcome!

ClareS [to Geraint] .. but you're an hour late ...

Geraint says "hello, here at last"

ClareS [to Geraint] I must go very soon - I'm afraid I have a RL meeting at 16

ClareS says "(type read may13tape)"
Gmocz It is 5am here. I can have an hour sleep before I need to go to work

ClareS says "thanks, Gmocz & Andy for a stimulating discussion"
ClareS turns the ClareS_recorder off.