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Special Topics

by: Jordane Kemmer

Special Topics ST 590

Jordane Kemmer
GPA 3.79


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Class Notes
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This 6 page Class Notes was uploaded by Jordane Kemmer on Thursday October 15, 2015. The Class Notes belongs to ST 590 at North Carolina State University taught by Staff in Fall. Since its upload, it has received 17 views. For similar materials see /class/223974/st-590-north-carolina-state-university in Statistics at North Carolina State University.

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Date Created: 10/15/15
CASP Critical Assessment of Structure Prediction Year Predictions Groups Targets CASP I 1994 635 35 33 CASP H 1996 947 76 42 CASP HI 1998 37807 98 43 CASP IV 2000 117136 125 56 CASPV 2002 287000 239 67 CASP VI 2004 347000 289 87 most of above data courtesy of Joturi Hein 111 CASP4 Results ie7 the stateof theart for fold recognition as of Dec 2000 These notes are summarized from a manuscript by M Sippl et al that can be found at httploreoamesbgaoatCASP experimentally determined but unreleased target protein structures 27 single domain proteins 11 two domain proteins 1 three domain protein 1 four domain protein 56 total domains 112 Domains were placed into categories according to Whether they had sequence similarity and or structural similarity to proteins that were in pdb Category Cll Comparative Modelling clear hit of target domain to sequence of pdb entry via psi blast 10 target domains Category CMFR Comparative Modelling Fold Recognition weak hit to sequence of pdb entry via psi blast 8 target domains Category FR H No recognizable sequence similarity but clear structural similarity to PDB entry Also7 conserved functional patterns77 can be recognized in the structural alignments 11 target domains Category FR A No recognizable sequence similarity but clear structural similarity to PDB entry 11 target domains Category FRNF Fold recognition New Fold No recognizable sequence similarity but some similarity to substructures of PDB entries 12 target domains Category NF No similarity recognized at either sequence or structural level to any PDB entries 4 target domains 113 Assessment of predictions for fold recognition exclude domains in CM7 CM FR7 and NF categories So7 there are 34 remaining targets for fold recognition For fold recognition7 each prediction received a score from 0 completely wrong to 2 correct fold7 bad alignment to 4 correct fold and correct alignment CASP4 miscellenea CASP4 assessment phase required about 52 person weeks of labor T total score7 summed over all predictions from group ranged from 415 David Baker group7 34 submissions and 40 Alexey lVlurZin7 16 submissions to O Q average score among predictions submitted by group were as high as the 25 achieved by the 16 predictions of Alexey MurZin 114 CAFASP Critical Assessment of Fully Automated Structure Prediction CAFASP was the portion of CASP where completely automated structure prediction routines were evaluated The highest CAFASP score was achieved by the Sternberg SDPSSM software which ranked number 12 in total score Ti and number 17 in average score QZ39 Subjective impressions of Sippl et al Between CASPS and CASP47 the standards among the best fold recognition groups have gotten higher 115 On the other hand Considering the large number of low total scores T it is fair to say that about two thirds of the predictors did not make any progress so that the community as a whole grew in number but on average not in erpertise Another way to look at this is that a large fraction of predictors scored worse than several dutomdted seruers The latter in a sense represent that part of prediction technology that can be cast in computer software 116


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