From mailer@bialko.llnl.gov Wed Aug 7 14:13:08 2002 Date: Wed, 7 Aug 2002 14:13:02 -0700 (PDT) From: Automatic Reply To: karplus@soe.ucsc.edu X-SpamBouncer: 1.4 (10/07/01) X-SBNote: From Admin X-SBNote: FROM_DAEMON/Listserv X-SBPass: No Freemail Filtering X-SBClass: Admin # # Protein Structure Prediction Center, LLNL, Livermore, CA # Verification system Wed Aug 7 13:45:12 PDT 2002 by Adam Zemla # # The PIN number of your submission is: PIN_575256_19625 # (PIN number is not an ACCESSION CODE) # Thank you for your submission. Your prediction has been accepted with an ACCESSION CODE: T0166SS007_1 Current information on models submitted in prediction T0166SS007 MODEL_INDEX PIN CODE DATE E-mail T0166SS007_1 PIN_575256_19625 6269-7633-6117 08/07/02 13:45:12 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 T0166 MODEL_INDEX PIN CODE DATE E-mail T0166SS007_1 PIN_575256_19625 6269-7633-6117 08/07/02 13:45:12 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 T0166 AUTHOR 6269-7633-6117 # 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: 150 # Number of residues with nonzero confidence: 150 # Number of METHOD records: 42 # No errors. ################################ # # # SUBMISSION # # # ################################ # # # BEGIN # # # ################################ PFRMAT SS TARGET T0166 AUTHOR 6269-7633-6117 METHOD CAFASP METHOD samt99 METHOD This prediction was derived from the following methods METHOD by averaging the corresponding probabilities: METHOD Method 0: METHOD TARGET seed-seqs-1119.a2m(1) METHOD Using neural net overrep-2500-IDaa13-5-9-7-10-5-9-11-ehl2-seeded2-stride-trained.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 9 METHOD 7 10 METHOD 5 9 METHOD 11 3 (1 EHL2 ) METHOD The input amino acid frequencies were determined from METHOD alignment /var/tmp/hmm-target99-work-4579//target-align-4579.a2m METHOD with weighted counts, using EntropyWeight(1.4 bits/column, 10) METHOD The weighting was determined by the posterior distribution METHOD after regularizing with /projects/compbio/lib/recode3.20comp. METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 276.784 METHOD METHOD CHAIN 1 METHOD Method 1: METHOD Prediction using SAM HMM nearest-neighbor METHOD sequence: seed-seqs-1119.a2m(1) METHOD model_file: /projects/compbio/tmp/sam-nn-tmp.cc66.11266/model.mod METHOD database_files: /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.seq /projects/compbio/programs/hmm-server-2.0/src/pcc/data/overrep-2260.verify.mixed.2d METHOD scoring_mode: local METHOD null_model: reverse METHOD scoring_algorithm: EM METHOD adjust_score: 2 METHOD date: Mon Aug 5 17:18:17 2002 METHOD Method 2: METHOD ###begin 0 METHOD METHOD Protein secondary structure prediction by universal HMM METHOD HMM file: /projects/compbio/programs/hmm-server-2.0/src/pcc/scripts/gdac.test.initreest.38state.abb.isites.gd.updated.ghmm-128reest-1-128-105-0.07gd METHOD Alignment file: /var/tmp/hmm-target99-work-4579//target-align-4579.a2m METHOD METHOD guide seq name: seed-seqs-1119.a2m(1), 150 bases, CC6A029D checksum. METHOD ###end 0 MODEL 1 V C 0.558 T H 0.485 D H 0.579 I H 0.685 L H 0.709 R H 0.729 E H 0.735 I H 0.754 G H 0.753 M H 0.757 I H 0.757 A H 0.76 R H 0.768 A H 0.758 L H 0.742 D H 0.737 S H 0.732 I H 0.714 S H 0.704 N H 0.699 I H 0.701 E H 0.678 F H 0.658 K H 0.618 E H 0.599 L H 0.447 S C 0.644 L C 0.63 T C 0.652 R H 0.595 G H 0.634 Q H 0.658 Y H 0.668 L H 0.67 Y H 0.673 L H 0.684 V H 0.678 R H 0.671 V H 0.66 C H 0.621 E H 0.565 N C 0.6 P C 0.669 G C 0.663 I C 0.616 I C 0.602 Q H 0.683 E H 0.721 K H 0.733 I H 0.742 A H 0.74 E H 0.738 L H 0.719 I H 0.657 K C 0.523 V C 0.589 D C 0.655 R H 0.554 T H 0.614 T H 0.646 A H 0.714 A H 0.735 R H 0.77 A H 0.769 I H 0.799 K H 0.804 R H 0.813 L H 0.804 E H 0.778 E H 0.765 Q H 0.613 G C 0.607 F C 0.416 I E 0.538 Y E 0.528 R E 0.465 Q C 0.428 E C 0.56 D C 0.682 A C 0.577 S C 0.579 N C 0.603 K C 0.561 K C 0.439 I E 0.417 K E 0.49 R E 0.579 I E 0.597 Y E 0.564 A E 0.46 T C 0.527 E H 0.464 K H 0.609 G H 0.64 K H 0.677 N H 0.694 V H 0.717 Y H 0.74 P H 0.758 I H 0.76 I H 0.749 V H 0.741 R H 0.753 E H 0.751 N H 0.751 Q H 0.77 H H 0.772 S H 0.766 N H 0.768 Q H 0.777 V H 0.771 A H 0.747 L H 0.727 Q H 0.662 G H 0.53 L C 0.563 S C 0.673 E H 0.741 V H 0.771 E H 0.785 I H 0.834 S H 0.844 Q H 0.846 L H 0.853 A H 0.864 D H 0.87 Y H 0.863 L H 0.87 V H 0.865 R H 0.857 M H 0.831 R H 0.809 K H 0.79 N H 0.751 V H 0.729 S H 0.676 E H 0.661 D H 0.546 W H 0.527 E H 0.495 F H 0.46 V C 0.446 K C 0.503 K C 0.535 G C 0.57 N C 0.573 T C 0.535 R C 0.535 N C 0.579 Y C 0.656 END ################################ # # # END # # # ################################