From mailer@bialko.llnl.gov Fri Aug 16 06:18:08 2002 Date: Fri, 16 Aug 2002 06:18:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBPass: NoBounce X-SBClass: OK # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Fri Aug 16 05:49:57 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_625740_25746 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0190SS389_1 Current information on models submitted in prediction T0190SS389 MODEL_INDEX PIN CODE DATE E-mail T0190SS389_1 PIN_625740_25746 1549-8716-6404 08/16/02 05:49:57 casp5@bialko.llnl.gov PLEASE NOTE: Submission of a duplicate prediction (same target, format, model index) will REPLACE an existing submission (ACCESSION CODE), provided it is received before the target has expired. The current status of models accepted for target T0190 MODEL_INDEX PIN CODE DATE E-mail T0190SS389_1 PIN_625740_25746 1549-8716-6404 08/16/02 05:49:57 casp5@bialko.llnl.gov For more information on accepted models submitted to CASP5 see: http://PredictionCenter.llnl.gov/casp5/models/casp5-models.html Please check below if the verified data of your submission is correct. # Reading prediction format SS PFRMAT SS TARGET T0190 AUTHOR 1549-8716-6404 # Reading MODEL 1 # Reading prediction format SS (DONE) # Checking the SS prediction MODEL 1 # Checking the SS prediction MODEL 1 (DONE) # MODEL index: 1 # Total number of residues in model: 114 # Number of residues with nonzero confidence: 114 # Number of METHOD records: 65 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0190 AUTHOR 1549-8716-6404 METHOD CAFASP METHOD samt02_dssp_ehl METHOD This file is the result of combining several RDB files, specifically METHOD T0190.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0190.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0190.t2k.str.rdb (weight 1.53983) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from T0190.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0190 METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0190.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 36 METHOD METHOD ============================================ METHOD Comments from T0190.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0190 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0190.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 36 METHOD METHOD ============================================ METHOD Comments from T0190.t2k.str.rdb METHOD ============================================ METHOD TARGET T0190 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 13 (1 str ) METHOD The input amino acid frequencies were determined from METHOD alignment T0190.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 36 METHOD METHOD ============================================ MODEL 1 A C 0.95 Q C 0.92 Q C 0.90 N C 0.89 I C 0.83 L C 0.52 S E 0.66 V E 0.87 H E 0.92 I E 0.91 L E 0.85 N E 0.65 Q C 0.52 Q C 0.70 T C 0.83 G C 0.89 K C 0.68 P C 0.61 A C 0.77 A C 0.84 D C 0.87 V C 0.66 T E 0.81 V E 0.95 T E 0.97 L E 0.97 E E 0.96 K E 0.92 K E 0.62 A C 0.81 D C 0.95 N C 0.92 G C 0.52 W E 0.76 L E 0.82 Q E 0.84 L E 0.82 N E 0.74 T E 0.68 A E 0.73 K E 0.74 T E 0.68 D C 0.88 K C 0.95 D C 0.95 G C 0.91 R C 0.67 I E 0.56 K C 0.74 A C 0.77 L C 0.73 W C 0.79 P C 0.81 E H 0.49 Q H 0.49 T C 0.51 A C 0.70 T C 0.71 T C 0.61 G E 0.54 D E 0.81 Y E 0.95 R E 0.97 V E 0.97 V E 0.96 F E 0.90 K E 0.62 T C 0.52 G H 0.78 D H 0.88 Y H 0.93 F H 0.94 K H 0.91 K H 0.78 Q C 0.67 N C 0.97 L C 0.96 E C 0.93 S C 0.81 F C 0.66 F C 0.60 P C 0.56 E C 0.50 I E 0.73 P E 0.90 V E 0.94 E E 0.97 F E 0.97 H E 0.93 I E 0.78 N C 0.54 K C 0.88 V C 0.93 N C 0.93 E C 0.80 H E 0.56 Y E 0.87 H E 0.92 V E 0.91 P E 0.86 L E 0.81 L E 0.82 L E 0.64 S C 0.72 Q C 0.80 Y C 0.72 G C 0.65 Y C 0.58 S C 0.54 T C 0.52 Y C 0.57 R C 0.74 G C 0.89 S C 0.97 END END ################################ # # # END # # # ################################