This file is a brief summary of the status of each target, and will be updated frequently. For more details about each target, see the README file from the appropriate subdirectory. P111 is SAM-T99 (Automatic server) P094 is SAM-T2k (hand predictions) target expires template scop notes t86 jul 20 2chsA 4.64.1.2.1 SUBMITTED (chosen based on paper by Stover et al) t87 sep 7 (8abp or 1bxkA) + 1be1 SUBMITTED Rossman fold+2nd domain. 3.88.1.1.2 or 3.2.1.2.2) and 3.16.5.1.2 We ended up with a Rossman fold, like everyone else, but have an ok 2nd domain prediction too. GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 6.35 20.08 (8th) 26.81 (Baker) DOMAIN 2 0 16.81 (36th) 28.45 (Baker) SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 0 1 2 (Braun-UTMB) DOMAIN 2 -- 0.5 1 (MPRAHBA) Must have been something wrong with the submission, since the same second domain was submitted for both models, but they were evaluated quite differently. Was first or second model was better for first domain? Sippl has T0087_1AL094_2_1 based on 1bxkA getting high eqr1 (but no score, since second model), would have been 4th best. Which model did better in GDT scoring? Second domain based on 1be1. t88 sep 7 1wkt or 1qtsA SUBMITTED 2 models. 2.10.1.3.1 or 2.1.9.1.1 Couldn't find an existing lectin that lined up well. t89 sep 1 1dkgD or 1ba1 SUBMITTED 2 very similar predictions 3.50.1.1.3 or 3.50.1.1.1 PDB=1e4fT CORRECT (at least at family level) Best FSSP hits: 1yagA (3.50.1.1.7), 1ba1 (3.50.1.1.1) GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 35.34 (6th) 21.21 37.24 (Jose) DOMAIN 2 42.79 52.40 (16th) 66.83 (Sternberg) DOMAIN 3 25.93 31.17 (6th) 36.42 (Vajda) DOMAIN 4 57.18 (22nd) 47.03 63.61 (Taylor) Second model not evaluated? T2K domain2 prediction missed part on C-terminus of domain 2 that others aligned. SIPPL SAM-T99 SAM-T2K BEST DOMAIN 2 0 0 0.5 (Friesner) t90 jul 6 1tum 4.94.1.1.1 SUBMITTED 2 alignments GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 0 15.62 (29th) 33.04 (Skolnick-Kolinksi2) DOMAIN 2 36.36 (30th) 17.48 45.98 (SBI-AT) Second alignment not evaluated. SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 0 N 2 t91 sep 8 1bmtA-1c3qA-1sesA SUBMITTED undertaker-assembled fragments SIPPL SAM-T99 SAM-T2K BEST 0 0 3 (Baker) t92 jul 22 1xvaA 3.61.1.2.1 SUBMITTED, some hand editing t93 Jul 22 1vid 3.61.1.1.1 SUBMITTED 1vid, based on web finds. t94 Aug 1 1yghA 4.89.1.1.4 SUBMITTED T0094-1yghA-global-edited PDB=1fsi (not in FSSP yet) SIPPL SAM-T99 SAM-T2K BEST 0 0 0.5 (Murzin, ...) t95 Sep 8 1dovA no-scop SUBMITTED 1dovA/T0095-1dovA-karplus.a2m, great 2ry match, is alpha-catenin. GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 16.04 48.96 (7th) 65.62 (Bioinfo) DOMAIN 2 20.87 39.05 (10th) 59.50 (Blundell-TL) SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 0 0.5 4 DOMAIN 2 0 3 4 Excellent alignment for the part of domain 1 I submitted, should have extended toward N-terminus. Not sure why Sippl rated it so low (should perhaps have used 1dowA instead of 1dovA?) OK, but not great alignment for domain 2. (Template not available in time for CAFASP.) t96 Sep 8 1qbjA 1.4.4.17.1 SUBMITTED just N-terminus T0096-1qbjA-karplus2 GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 57.08 62.84 (6th) 67.57 (Murzin) DOMAIN 2 7.26 0 28.72 (Jones-AB) SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 3.5 4 4.5 DOMAIN 2 0 - 1 (ORNL Prospect, ... ) t97 Aug 31 1aj8A? 1.98.1.1.3 SUBMITTED T0097-1aj8A-local.pw.a2m.gz SIPPL SAM-T99 SAM-T2K BEST 0 0 1.5 (Baker) t98 Aug 15 1bxm+1ebmA No good hits. SUBMITTED undertaker which pasted together 1bxm and 1ebmA. 1.125.1.1.1+? PDB=1fc3A (new fold? 1a04A has Z score 5.5) First two helices look good---rest has poor match. SIPPL SAM-T99 SAM-T2K BEST 0 0 2 (Sternberg) t99 Jul 25 5hct 2.32.2? SUBMITTED monomeric SH3, gapless alignment t100 Jul 3 1qcxA or 1rmg SUBMITTED 2 BETA-HELIX ALIGNMENTS 2.75.1.2.2 or 2.75.1.4.1 PDB=1qjvA CORRECT, FSSP matches 1bhe 17.4, 1pcl 17.2, 1qcxA 16.7, 1air 15.8, 1rmg 14.9 SIPPL SAM-T99 SAM-T2K BEST 0 3.5 4 (Baker and Murzin) First model (1qcxA) slightly better. SAM-T99 correct hit was number 8 (3rd superfamily). Correct fold selected by functional match and by CAFASP hits. Would 2track have helped? t101 Sep 11 1dbgA or 1czfA SUBMITTED T0101-1dbgA-karplus2 based on 2-track alignment (and 1czfA-T0101-fssp-global) 2.75.1.6.1 or 2.75.1.4.3 CORRECT t102 Aug 30 ??? SUBMITTED 2ry only. CYCLIC polypeptide, no hits. PDB=1e68A t103 Sep 11 1sup 3.35.1.1.7 SUBMITTED 1sup/1sup-T0103-karplus.a2m t104 Sep 11 1d2mA 3.31.1? SUBMITTED T0104-1d2mA-karplus2.a2m t105 Aug 31 ??? SUBMITTED fragment 1a02N-T0105-local t106 Jul 25 new fold SUBMITTED NEW FOLD, no ab initio prediction t107 Aug 29 1ema 4.20.1.1.1 SUBMITTED 1ema-T0107-karplus.a2m t108 Sep 1 1b9mA SCOP? SUBMITTED weak (2-track only) prediction LOOKS WRONG. Got domain boundaries right. Could have, but didn't, predict 2nd domain as single helix. t109 Sep 1 1cxqA 3.50.3.2.1 SUBMITTED T0109-1cxqA-karplus1 t110 Sep 12 1egaA+1lehA SUBMITTED undertaker composite of 2 super-scondary matches. The 1egaA match good, the 1lehA match no extra value, but first helix shifted by 2 turns, SIPPL SAM-T99 SAM-T2K BEST 0 3 3 The 1egaA match was 4th on the 2track list, and earlier hits (other than 1lehA) were eliminated by compactness of sheets. t111 Sep 12 2one[AB] SUBMITTED two undertaker files. close enough for molecular replacement 3.1.10.1.1,4.45.1.1.1 GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 86.91 88.09 (~45th) 93.95 (Venclovas) DOMAIN 2 86.26 (36th) 83.44 90.98 (Wolynes) First domain, in the large group which has an 8Ang error about 1/3 of the way through (best groups used 4enl as tempate). Only first model evaluated. t112 Aug 31 1ykfA SUBMITTED 1ykfA/1ykfA-T0112-global-karplus2.a2m 2.33.1.2.4,3.2.1.1.4 GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 67.39 67.61 (27th) 73.64 (Venclovas) DOMAIN 2 76.69 (2nd) 73.63 82.62 (Venclovas) t113 Aug 4 2hsdA 3.2.1.2.12 SUBMITTED 2hsdA/T0113-2hsdA-global-edited t114 Aug 4 1hoe? 2.4.1.1.1 SUBMITTED T0114-1hoe-2track-global (not a great hit) t115 Sep 12 1b6cB 4.123.1.1 SUBMITTED 1b6cB/T0115-1b6cB-karplus1.a2m and T0115-family.2d Template choice based on 2-track and functional info. GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 13.72 13.87 (29th) 20.43 (GNM-FR) DOMAIN 2 16.67 20.64 (3rd) 22.16 (JONES) t116 Aug 31 2tgoA + 1b0uA SUBMITTED 2 domains. 1b0uA good. ? + 3.31.1.11.1 Initial domain match very dubious. PDB=1ewqA (2tgoA ok---though badly misaligned) GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 0 0 30.47 (Baker) DOMAIN 2 0 20.04 (7th) 36.98 (Baker) DOMAIN 3 0 8.96 (23rd) 13.23 (Bintohes) DOMAIN 3A 0 15.81 (8th) 22.44 (Baker) DOMAIN 3B 0 16.09 (19th) 27.91 (Baker) DOMAIN 4 26.04 (6th) 27.65 (4th) 30.53 (Sternberg) DOMAIN 4 good score is for the second chain (1b0uA) Question: why are GDT scores higher for subdomains---this looks like a misalignment error for evaluating domain 3. (NOPE---my misunderstanding of GDT normalization.) Note: 1b0uA was pointed out as homology by submitters (ABC transporter ATPase), but I didn't notice! t117 Sep 13 5tmpA 3.31.1.1.16 SUBMITTED 5tmpA---best 2-track hit. t118 Sep 13 1avqA 3.47.1.9.1 SUBMITTED T0118-act-1avqA-karplus2.a2m t119 Sep 13 1czpA+1qfjA SUBMITTED 2 separate domains. strong homologs. 4.13.6.1.1+(2.41.1.1.6,3.18.1.1.6) Pasted together 2ry predictions. t120 Sep 14 1dzkA,1dceA,1svy,1bs2A,1ckqA SUBMITTED 5 models There seem to be three domains. Most hits for first domain. GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 0 14.87 (33rd) 24.57 (Baker) DOMAIN 2 37.07 37.36 (16th) 78.45 (Onizuka) SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 0 1 2 (Baker) DOMAIN 2 0 0 4.5 (mrit-onizuka, 1cii) For first domain, what model best? For second domain, first model 1dkzA best. t121 Sep 14 1b0uA+1b9mA SUBMITTED two domains 3.31.1.11.1+? pasted together 2ry prediction. PDB=1eu8 (not in FSSP yet) 2nd domain correct GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 74.12 (22nd) 69.26 76.18 (SBFOLD) DOMAIN 2 0 61.36 (2nd) 68.56 (Murzin) DOMAIN 3 92.50 (3rd) 92.50 (3rd) 93.21 (bioingbu-seqpmprf) Split domain 1 1-87, 158-240 caused some confusion. Almost everyone got domain 3 (88-157). SAM-T99 missed domain 2 (241-372). SIPPL SAM-T99 SAM-T2K BEST DOMAIN 2 -- 4 4.5 (Murzin) SAM-T99 lost because it did not try to predict domain 2. SAM-T2k had right domain boundary and got decent prediction for second domain. t122 Sep 14 2tysA 3.1.2.2.5 SUBMITTED T0122-2tysA-karplus.a2m t123 Sep 15 1dv9A 2.56.1 SUBMITTED try7/t123-opt.pdb PDB=1exsA (CORRECT, but is it best template?) both 1exsA and 1dv9A are in 1bebA FSSP file (60% id) t124 Sep 15 ??? SUBMITTED 2ry and undertaker-built mini-threading. Structure is all long helices, but fold is completely bogus. t125 Sep 15 3lynA SUBMITTED try3/t125-opt.pdb sigh, they told us the homology, and I was so proud of having found it! Undertaker resolved several alignments. t126 Sep 15 1atzA 3.57.1 SUBMITTED T0126-1atzA-karplus1.a2m as the best of a bad lot. SIPPL SAM-T99 SAM-T2K BEST 0 2.5 t127 Sep 15 1do0A 3.31.1 SUBMITTED T0127-1do0A-karplus.a2m GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 32.46 33.27 (5th) 39.11 (SBfold) DOMAIN 2 30.06 40.18 (2nd) 41.96 (UCLA-DOE) T99 alignment for domain 2 more precise than T2k alignment, but ends too soon. SIPPL SAM-T99 SAM-T2K BEST DOMAIN 1 3 3 3 DOMAIN 2 1.5 2.5 2.5 t128 Sep 15 1avmA 1.2.7?4.38.1 SUBMITTED undertaker based on T0128-1avmA-karplus.a2m GDT_TS SAM-T99 SAM-T2K BEST DOMAIN 1 85.51 86.08 (>40th) 98.01 (Levitt) DOMAIN 2 87.20 89.63 (49th) 94.31 (Ginalski) Best groups used 1b06A as template, not 1avmA. Looks like I guessed wrong on the template choice---it was a tossup which one to use. I should have believed the evolutionary tree more.