4 Predicting: Expected quality of a model (QMode 1) Protein structure Quality prediction:The casp initiativePredicting:Expected quality of a model (QMode 1)Expected error on residue Cα (QMode 2)Quoting the CASP web page:You may submit your quality assessment prediction in one of the two different modes: QMODE 1 : global model quality score (MQS - one number for a model) QMODE 2 : MQS and error estimate on per-residue basis.
12 Maistas: http://www.bioinformatica.crs4.org taking splicing into account
13 Maistas: taking splicing into account Maistas output Server output are three-dimensional coordinates in PDB format for each modelled peptide and a table describing results of the structural analysis.Then all models are analyzed in terms of their suitability to exist in the monomeric state. When model check!! warning appears in the output report we cannot exclude the possibility that they take some other multimeric state for stabilizing.Moreover, as a model is built, splicing isoform exonic coordinates are mapped on it. A PyMol script is created too, so the user can easily visualize exon mapping on protein model with different colours.
17 ANTIBODIES: 94 95 Pro 90 Gln Chothia et al., Nature 1989 A different story95Pro90Gln94* ** *Y Q S L P Y QW T Y P L I QChothia et al., Nature 1989
18 Canonical structures for the ‘torso’ of H3: ANTIBODIES:A different storyCanonical structures for the ‘torso’ of H3:94R – 101D101101949410310394 non R or 101 non DMorea et al., JMB., 1998
19 ANTIBODIES: target sequence BLAST VL template TL Align Build framework A different storytarget sequenceBLASTVL templateTLAlignBuild framework
20 ANTIBODIES: target sequence BLAST VL template TL Align Build framework A different storytarget sequenceBLASTVL templateTLAlignBuild framework
21 ANTIBODIES: Ab VL sequence Ab VH sequence target sequence “BLAST” A different storyAb VL sequenceAb VH sequencetarget sequence“BLAST”BLASTVL templateTLVH templateTHtemplate“Align”AlignTL=TH?Fit conservedinterfaceBuild templateBuild frameworkBuild framework
22 ANTIBODIES: Ab VL sequence Ab VH sequence “BLAST” VL template TL A different storyAb VL sequenceAb VH sequence“BLAST”VL templateTLVH templateTH“Align”TL=TH?Fit conservedinterfaceBuild templateBuild framework
23 Taking the frameworks from different structures introduces errors ANTIBODIES:A different storyTaking the frameworks from different structures introduces errorsOne might be better off selecting the same template, at the cost of loosing in sequence identity
24 Taking the loops from different structures introduces errors ANTIBODIES:A different storyTaking the loops from different structures introduces errorsOne might be better off selecting a template with the right CS, at the cost of loosing in sequence identity
25 Same antibody and canonical structures Same canonical structures ANTIBODIES:A different storySame antibodySame antibody and canonical structuresSame canonical structuresBest Vl and Vh