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PDB ID Mentions in PubMed Central Article count: 15

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PDB ID Mentions in PubMed Central

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Amino acid empirical contact energy definitions for fold recognition in the space of contact maps.

(2003) BMC Bioinformatics 4

PubMed: 12689348 | PubMedCentral: PMC153506 | DOI: null

Figure 9 Energy vs. RMSD for 4pti 4state decoys The contact energy is plotted against the RMSD from native structure for native structure and all decoy structures with solvent accesibility parameter l... wer than 0.6 (see text).

Publication Year: 2003


Scoring predictive models using a reduced representation of proteins: model and energy definition.

(2007) BMC Struct Biol 7

PubMed: 17378941 | PubMedCentral: PMC1854906 | DOI: 10.1186/1472-6807-7-15

rank native RMSD Z-score cc F.E. lmds 1b0n-B 1/498 0.0 -3.3 0.05 18.4 lmds 1bba 501/501 4.5 21.4 -0.23 10.0 lmds 1ctf 1/498 0.0 -3.4 0.31 2.0 lmds 1dtk 2/216 6.3 -2.5 0.21 33.3 lmds 1fc2-C 53/501 5.4 ... 1.3 0.17 24.0 lmds 1igd 1/501 0.0 -4.0 0.10 6.0 lmds 1shf-A 1/438 0.0 -5.3 0.11 11.6 lmds 2cro 1/501 0.0 -7.7 0.13 20.0 lmds 2ovo 1/348 0.0 -3.2 0.11 5.9 lmds 4pti 1/344 0.0 -3.5 0.02 14.7 Table 9 Performance evaluation of the energy function on semfold decoy set Decoy set PDB id.

rank native RMSD Z-score cc F.E. 4state_reduced 1ctf 1/631 0.0 -3.4 0.59 58.7 4state_reduced 1r69 1/676 0.0 -4.0 0.62 47.8 4state_reduced 1sn3 1/660 0.0 -3.6 0.36 34.8 4state_reduced 2cro 1/674 0.0 -3.2 0.69 55.2 4state_reduced 3icb 1/654 0.0 -2.9 0.76 70.8 4state_reduced 4pti 1/687 0.0 -3.1 0.40 33.8 4state_reduced 4rxn 667/677 2.1 2.5 0.48 46.3 Table 2 Performance evaluation of the energy function on fisa decoy set Decoy set PDB id rank native RMSD Z-score cc F.E. fisa 1fc2-C 1/501 0.0 -6.6 0.11 12.0 fisa 1hdd-C 1/501 0.0 -8.4 0.24 16.0 fisa 2cro 1/501 0.0 -7.3 0.17 22.0 fisa 4icb 1/500 0.0 -9.3 0.23 22.0 Table 3 Performance evaluation of the energy function on fisa_casp3 decoy set Decoy set PDB id.

Publication Year: 2007


Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

(2007) BMC Bioinformatics 8

PubMed: 17662112 | PubMedCentral: PMC2034607 | DOI: 10.1186/1471-2105-8-270

PDB ID a 20Cl OS1 b 20Cl OS2 6Cl OS2 4Cl OS2 Lu c Bastolla c 1AVZ 73 35 67 100 54 40 1BGS 1 65 62 39 16 1 1BRC 76 37 41 31 5 70 1CGI 56 1 1 1 1 18 1DFJ 100 100 100 100 78 100 1FSS 24 1 1 1 1 1 1UGH 11... 10 20 10 10 71 1WQ1 99 100 100 100 97 98 2PCC 20 72 82 79 25 23 2SIC 17 48 56 17 14 96 5CHA - 2OVO 6 7 3 2 2 3 2PTN - 4PTI 5 9 9 33 4 10 1SUP - 2CI2 4 4 4 4 5 9 1A2P - 1A19 31 58 52 27 20 17 1CHG - 1HPT 2 7 4 6 2 4 T04 9 8 10 11 11 1 T05 64 61 62 62 60 60 T06 2 3 3 1 4 3 T07 58 63 62 56 58 64 T08 84 52 68 96 136 145 T09 165 162 164 165 159 164 T11 1 1 2 1 1 1 T12 9 5 6 2 1 5 T13 194 176 179 175 174 175 T14 68 121 91 125 18 43 T15 12 3 4 7 1 1 T18 25 8 7 1 2 4 T19 3 38 22 1 37 6 Our energy function was more successful with the Vakser set, with one failure and four successes (native structure among the top ten).

Publication Year: 2007


Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design.

(2008) BMC Bioinformatics 9

PubMed: 18366628 | PubMedCentral: PMC2292695 | DOI: 10.1186/1471-2105-9-148

These structures were extracted from various positions in the X-ray structures of 6 different proteins taken from the PDB [ 54 ]: lysozyme (2LZM), bovine pancreatic trypsin inhibitor (4PTI), staphyloc... ccal nuclease (1STN), α -toxin (1PTX), ribonuclease A (2RN2) and cyclophilin (2CPL).

Publication Year: 2008


Identification of hot-spot residues in protein-protein interactions by computational docking.

(2008) BMC Bioinformatics 9

PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447

Table 6 Additional dataset of complexes used in this work Complex a Res b Receptor Ligand Receptor PDB Res (Id) b Ligand PDB Res(Id) b Complex type c X-ray subunits 1CBW 2.60 Chymotrypsin BPTI 4CHA 1.... 8 4PTI 1.50 U/U 1PM9 1.70 IL-6R IL-6 1N26 2.40 1ALU 1.90 U/U N/A N/A KDR VEGF 2P2H 1.95 1VFP 2.50 U/U N/A N/A trkC Neurotrophin-3 1WWC 1.90 1NT3 2.40 U/U 2BTF 2.55 Rabbit actin Bovine profilin I 1J6Z 1.54 1PNE 2.00 U/U 1DVF 1.90 E5.2 D1.3 - - 1VFA 1.80 B/U N/A N/A sHIR Insulin 2DTG 3.80 2C8Q 1.95 U/U NMR subunits N/A N/A GPIIbIIIa Kistrin 1TYE 2.90 1N4Y NMR U/U N/A N/A bFGF FGFR1b 4FGF 1.60 1WVZ NMR U/U N/A N/A IGF-1R IGF-1 1IGR 2.60 2GF1 NMR U/U N/A N/A IGF-1bp IGF-1 1ZT3 1.80 2GF1 NMR U/U Homology-based modeled subunits N/A N/A E9 DNase Im2 1FSJ 1.80 1FR2 d (66%) U/M N/A N/A AChR Erabutoxin 2BG9 4.00 5EBX 2.00 cryo- EM/U N/A N/A AChR NmmI 2BG9 4.00 1V6P 0.87 cryo- EM/U 1Z92 2.80 IL-2 receptor IL-2 (human) 2B5I d (100%) 1M47 1.99 M/U N/A N/A IL-2 beta receptor(human) IL-2 (murine) 2B5I d (99%) 1M48 d (64%) M/M N/A N/A IL-2 alpha receptor(murine) IL-2 (murine) 1NWV d (22%) 1M48 d (64%) M/M N/A N/A IL-4/IL-4bp GammaC 1IAR 2.30 2B5I d (99%) U/M N/A N/A gp75 Neurotrophin-3 1LNL d (18%) 1NT3 2.40 M/U N/A N/A CD48 CD2 2DRU d (39%) 1CDC 2.00 M/U N/A N/A Calcineurin CaM 1AUI d (59%) 1LKJ NMR M/U 2D9Q 2.80 hG-CSFbp hG-CSF 2D9Q d (99%) 1RHG 2.20 M/U a PDB Code; N/A, Not Available; b Resolution in Å or (Id): sequence identity with template in case of model; c B, Bound; U, Unbound; M, Model; cryo-EM, cryoelectron microscopy structures classified as modeled structures because of the low resolution compared to crystallographic or NMR structures, d PDB code of the template structure used for modelling However, only a few of the 94 known hot-spots were detected, so the corresponding sensitivity ( S = 15%) was lower than that of the initial dataset ( S = 24%).

Publication Year: 2008


A knowledge-based structure-discriminating function that requires only main-chain atom coordinates.

(2008) BMC Struct Biol 8

PubMed: 18957132 | PubMedCentral: PMC2600639 | DOI: 10.1186/1472-6807-8-46

protein N R nat C α RMSD Z-score C.C. F.E.(%) R B1 logP B1 R B10 logP B10 C.C. decoy F.E. decoy (%) 4state_reduced 1ctf 631 1 0.000 4.485 0.817 68.3 61 -1.01 3 -2.32 0.815 66.7 2cro 675 1 0.00... 3.166 0.822 53.7 7 -1.98 2 -2.53 0.820 53.7 4rxn 678 1 0.000 2.895 0.670 65.7 71 -0.98 3 -2.35 0.665 64.2 Average 661.3 1.0 0.000 3.515 0.770 62.6 46.3 -1.33 2.7 -2.40 0.767 61.5 fisa 2cro 501 1 0.000 4.190 0.280 24.0 3 -2.22 2 -2.40 0.253 24.0 Average 501.0 1.0 0.000 4.190 0.280 24.0 3.0 -2.22 2.0 -2.40 0.253 24.0 fisa_casp3 1bl0 972 8 5.522 2.174 0.302 20.6 15 -1.81 15 -1.81 0.296 19.6 l30 1401 1 1.882 3.835 0.128 18.6 455 -0.49 3 -2.67 0.111 17.9 Average 1186.5 4.5 3.702 3.005 0.215 19.6 235.0 -1.15 9.0 -2.24 0.204 18.7 hg_structal 1bab-B 30 1 0.000 1.868 0.904 66.7 10 -0.46 2 -1.16 0.892 0.0 1ecd 30 1 0.000 1.364 0.896 100.0 2 -1.16 2 -1.16 0.898 50.0 1gdm 30 1 0.000 2.395 0.880 33.3 4 -0.86 2 -1.16 0.845 0.0 1hbh-B 30 1 0.000 1.205 0.893 33.3 6 -0.68 2 -1.16 0.888 0.0 1hlb 30 1 0.000 1.661 0.812 33.3 15 -0.29 2 -1.16 0.812 0.0 1ith-A 30 1 0.000 1.775 0.904 33.3 23 -0.10 2 -1.16 0.893 0.0 1mbs 30 18 1.823 -0.270 0.754 33.3 3 -0.99 2 -1.16 0.835 0.0 1myt 30 1 0.000 2.429 0.762 100.0 2 -1.16 2 -1.16 0.725 50.0 2lhb 30 1 0.000 1.976 0.563 33.3 12 -0.38 4 -0.86 0.460 0.0 4sdh-A 30 1 0.000 3.221 0.839 33.3 21 -0.14 2 -1.16 0.750 0.0 Average 30.0 2.7 0.182 1.762 0.821 50.0 9.8 -0.62 2.2 -1.13 0.800 10.0 ig_structal 1bbd 61 1 0.000 2.304 0.605 16.7 27 -0.35 10 -0.78 0.554 0.0 1dfb 61 7 1.854 0.864 0.530 16.7 12 -0.70 4 -1.18 0.528 16.7 1fai 61 4 1.736 1.172 0.481 16.7 13 -0.66 4 -1.18 0.462 0.0 1fig 61 59 1.702 -2.283 0.349 0.0 21 -0.46 6 -1.00 0.504 0.0 1fpt 61 2 1.333 1.358 0.583 33.3 8 -0.88 4 -1.18 0.565 16.7 1fvd 61 1 0.000 2.112 0.606 16.7 22 -0.44 2 -1.48 0.574 0.0 1gig 61 1 0.000 2.787 0.547 16.7 10 -0.78 10 -0.78 0.469 0.0 1iai 61 1 0.000 2.103 0.644 33.3 8 -0.88 2 -1.48 0.613 16.7 1igf 61 2 1.774 1.353 0.607 16.7 31 -0.29 8 -0.88 0.591 0.0 1ikf 61 1 0.000 2.561 0.592 33.3 8 -0.88 3 -1.30 0.540 16.7 1jhl 61 1 0.000 1.380 0.333 16.7 41 -0.17 5 -1.08 0.286 0.0 1mcp 61 1 0.000 2.143 0.623 66.7 3 -1.30 2 -1.48 0.585 50.0 1mrd 61 1 0.000 2.305 0.379 16.7 51 -0.07 7 -0.93 0.264 0.0 1ngq 61 1 0.000 2.716 0.543 33.3 2 -1.48 2 -1.48 0.456 16.7 1opg 61 1 0.000 2.175 0.575 33.3 44 -0.14 3 -1.30 0.529 33.3 1tet 61 1 0.000 2.323 0.567 33.3 4 -1.18 4 -1.18 0.523 16.7 1vge 61 1 0.000 2.766 0.208 16.7 45 -0.13 26 -0.36 -0.020 0.0 2fb4 61 1 0.000 2.277 0.486 16.7 32 -0.27 13 -0.66 0.422 0.0 3hfl 61 1 0.000 2.648 0.243 33.3 29 -0.32 4 -1.18 0.055 16.7 7fab 61 1 0.000 2.941 0.614 50.0 6 -1.00 3 -1.30 0.531 33.3 Average 61.0 4.5 0.420 1.900 0.506 25.8 20.9 -0.62 6.1 -1.11 0.452 11.7 ig_structal_hires 1fgv 20 1 0.000 2.310 0.724 50.0 6 -0.50 2 -0.98 0.633 0.0 1gaf 20 1 0.000 2.827 0.649 50.0 8 -0.38 2 -0.98 0.493 0.0 1kem 20 1 0.000 1.518 0.636 50.0 11 -0.24 3 -0.80 0.567 0.0 1nbv 20 10 1.719 0.169 0.399 0.0 7 -0.43 4 -0.68 0.452 0.0 1vge 20 1 0.000 2.334 0.385 50.0 15 -0.10 2 -0.98 -0.116 0.0 2fbj 20 1 0.000 2.532 0.725 50.0 5 -0.58 2 -0.98 0.614 0.0 8fab 20 1 0.000 2.487 0.295 50.0 17 -0.05 8 -0.38 -0.228 0.0 Average 20.0 2.3 0.246 2.025 0.545 42.9 9.9 -0.33 3.3 -0.82 0.345 0.0 lattice_ssfit 1dkt-A 1995 1 0.000 7.349 -0.049 8.5 996 -0.30 242 -0.92 -0.087 8.0 1pgb 1997 1 0.000 13.649 0.138 17.1 1909 -0.02 60 -1.52 0.087 16.6 Average 1996.0 1.0 0.000 10.499 0.045 12.8 1452.5 -0.16 151.0 -1.22 0.000 12.3 lmds 1b0n-B 498 1 0.000 2.819 0.066 20.4 336 -0.17 10 -1.70 0.038 18.4 1dtk 216 70 7.224 0.375 0.044 4.8 42 -0.71 24 -0.95 0.038 4.8 1shf-A 437 1 0.000 4.275 0.064 11.6 378 -0.06 2 -2.34 -0.004 9.3 4pti 344 3 9.434 2.570 0.098 23.5 220 -0.19 4 -1.93 0.063 20.6 Average 373.8 18.8 4.165 2.510 0.068 15.1 244.0 -0.28 10.0 -1.73 0.034 13.3 semfold 1eh2 11442 61 12.125 2.342 0.070 13.6 6511 -0.25 434 -1.42 0.069 13.5 1pgb 11282 1 0.000 7.782 0.096 19.2 2 -3.75 2 -3.75 0.091 19.2 Average 11362.0 31.0 6.063 5.062 0.083 16.4 3256.5 -2.00 218.0 -2.59 0.080 16.3 moulder 1c2r 301 1 0.000 2.803 0.774 73.3 10 -1.48 2 -2.18 0.768 70.0 1cid 301 1 0.000 2.759 0.753 53.3 38 -0.90 2 -2.18 0.748 53.3 1gky 300 1 0.000 4.713 0.828 90.0 11 -1.43 3 -2.00 0.819 89.7 1mup 301 1 0.000 1.993 0.847 73.3 11 -1.44 3 -2.00 0.845 73.3 2cmd 301 1 0.000 2.506 0.911 36.7 15 -1.30 6 -1.70 0.911 33.3 2pna 301 85 3.523 0.723 0.816 66.7 30 -1.00 4 -1.88 0.817 66.7 8i1b 301 1 0.000 2.106 0.842 46.7 16 -1.27 4 -1.88 0.840 46.7 Average 300.9 13.0 0.503 2.515 0.824 62.9 18.7 -1.26 3.4 -1.97 0.821 61.9 rosetta 1a68 141 1 0.000 2.608 0.624 64.3 11 -1.11 3 -1.67 0.608 64.3 1aiu 141 15 1.385 0.805 0.777 7.1 40 -0.54 25 -0.75 0.776 7.1 1bk2 141 1 0.000 2.562 0.820 78.6 14 -1.00 3 -1.67 0.812 78.6 1bq9 141 2 9.242 1.895 0.544 50.0 131 -0.03 2 -1.85 0.532 50.0 1cc8 141 1 0.000 3.317 0.848 64.3 11 -1.11 2 -1.85 0.851 57.1 1ctf 141 1 0.000 4.288 0.783 28.6 30 -0.67 6 -1.37 0.780 28.6 1elw 141 22 3.619 1.082 -0.063 7.1 132 -0.03 12 -1.07 -0.070 7.1 1eyv 141 1 0.000 3.194 0.587 35.7 22 -0.80 2 -1.85 0.564 35.7 1gvp 141 1 0.000 3.018 0.540 21.4 61 -0.36 15 -0.97 0.514 21.4 1iib 141 1 0.000 6.093 0.595 71.4 9 -1.19 2 -1.85 0.629 71.4 1lou 141 1 0.000 2.664 0.741 71.4 8 -1.24 3 -1.67 0.731 64.3 1pgx 141 1 0.000 2.232 0.821 35.7 75 -0.27 5 -1.45 0.820 28.6 1rnb 141 8 13.461 1.445 0.440 21.4 89 -0.20 14 -1.00 0.427 21.4 1ten 141 1 0.000 4.986 0.866 92.9 5 -1.45 2 -1.85 0.876 85.7 1tul 141 5 0.842 2.002 0.763 64.3 16 -0.94 3 -1.67 0.755 57.1 1urn 141 1 0.000 2.452 0.694 64.3 9 -1.19 3 -1.67 0.680 57.1 1vie 141 1 0.000 3.470 0.791 71.4 2 -1.85 2 -1.85 0.781 71.4 256b 141 1 0.000 4.974 0.426 7.1 118 -0.07 42 -0.52 0.390 0.0 2ci2 141 80 10.219 0.075 -0.020 0.0 123 -0.06 71 -0.30 -0.022 0.0 Average 141.0 7.6 2.040 2.798 0.609 45.1 47.7 -0.74 11.4 -1.41 0.602 42.5 The performance scores for respective PDB IDs of the target proteins and their average are shown by individual generation methods.

decoy set protein DFIRE-A DFIRE-B DOPE RAPDF PC2CA DFMAC 4state_reduced 1ctf 1 1 1 1 1 1 4state_reduced 2cro 1 2 1 1 1 1 4state_reduced 4rxn 1 19 1 1 667 1 fisa 2cro 1 1 1 14 1 1 fisa_casp3 1bl0 1 3 1 1 1 8 lattice_ssfit 1dkt-A 1 1 1 1 1 1 lattice_ssfit 1pgb 1 1 1 1 1 1 lmds 1b0n-B 430 261 34 359 1 1 lmds 1dtk 1 5 1 116 2 70 lmds 1shf-A 1 1 1 1 1 1 lmds 4pti 1 1 1 157 1 3 average 40.0 26.9 4.0 59.4 61.6 8.1 correct 10 6 10 7 9 8 The rank of the native structure identified by respective functions is shown for the targets listed.

The IDs were 1bl0, 1dtk, 4pti, 1eh2, 2pna, 1bq9, 1elw, 1rnb, and 2ci2.

Publication Year: 2008


Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations.

(2009) BMC Struct Biol 9

PubMed: 19917096 | PubMedCentral: PMC2783033 | DOI: 10.1186/1472-6807-9-71

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 1eh2 6,06 4,64 1,64 4,93 4,13 4,93 1bg8 -A 7,84 7,28 7,28 3,58 5,72 3,58 1jwe 6,30 10,62 9,75 8,10 9,52 8,10 1bl0 4,10 2,24 2,24 7,10 4,45 7,10 s... d3 4,35 6,44 5,08 5,12 5,32 4,47 Average 5,73 6,25 5,20 5,76 5,83 5,63 lmds 1dtk 5,46 4,75 4,59 4,59 4,89 2,90 1igd 7,64 1,63 4,28 5,61 4,50 5,61 2cro 8,68 8,95 6,14 10,01 5,93 9,48 smd3 4,35 4,52 2,68 5,52 2,50 5,52 1ctf 9,41 7,65 7,52 7,37 6,67 7,37 1fc2 0,26 0,51 1,00 0,07 1,51 0,07 1shf -A 5,83 5,16 3,06 6,91 5,24 6,91 4pti 5,64 5,72 9,91 4,61 9,54 4,61 2ovo 6,92 3,49 6,45 5,70 7,26 5,70 1b0n -B 1,60 2,20 0,61 0,50 1,76 0,50 1bba 1,89 0,87 0,59 3,29 2,00 1,92 Average 5,24 4,13 4,26 4,92 4,71 4,60 4state_reduced 1sn3 1,69 0,90 4,09 4,71 6,05 0,90 1r69 2,55 0,80 0,79 0,95 2,29 0,79 4pti 0,82 5,53 0,07 0,07 1,18 2,80 2cro 2,46 1,24 0,29 1,24 0,53 0,53 1ctf 0,33 0,60 0,50 2,93 1,02 1,02 3icb 1,86 1,51 0,93 0,11 0,05 0,11 4rxn 0,46 3,52 0,75 0,70 0,68 0,70 Average 1,45 2,01 1,06 1,53 1,69 0,98 MOULDER 1onc 1,16 0,72 0,60 0,40 0,40 0,40 1dxt 3,97 0,00 0,55 1,11 0,00 0,55 1eaf 0,34 1,72 1,72 0,47 0,99 0,47 1lga 0,82 5,89 5,89 0,80 0,00 0,80 1gky 0,57 0,34 0,57 0,57 0,62 0,57 1cau 3,89 1,95 0,42 0,42 0,07 0,42 4sbv 0,00 5,57 0,00 0,00 6,43 0,00 8i1b 0,38 0,42 0,39 0,50 0,36 1,04 2mta 0,31 0,57 0,21 0,63 0,32 0,63 2cmd 0,38 2,22 0,58 0,23 0,74 0,84 2fbj 0,26 2,80 0,32 0,91 0,51 0,91 1cew 2,06 2,73 2,73 3,47 3,73 3,47 2afn 0,71 0,75 0,68 0,12 0,50 0,12 2sim 1,21 0,42 0,46 0,16 1,13 0,16 1bbh 0,88 0,11 0,16 0,00 0,31 0,00 1mdc 0,03 0,74 6,85 0,16 0,00 0,16 1mup 0,53 0,17 0,67 0,67 0,32 0,46 2pna 0,26 0,60 0,42 0,24 0,26 0,24 1cid 1,15 1,15 1,15 0,08 1,15 1,15 1c2r 3,42 0,00 0,85 0,00 0,00 0,15 Average 1,12 1,44 1,26 0,55 0,89 0,63 In the first column it is shown the code of the target protein used to generate the set of decoys.

Target set DOPE GA341 Prosa2003 DFIRE ZEmin fisa_casp3 smd3 1 51 2 1 12 1 1bg8 -A 1 808 151 1 341 2 1jwe 1 135 4 1 514 1 1eh2 8 826 93 1 577 159 1bl0 1 809 729 1 458 3 Total 4 0 0 5 0 2 lmds smd3 1 15 1 1 1 1 2ovo 7 33 1 61 115 7 1dtk 1 1 1 1 77 33 4pti 6 7 1 24 25 10 1b0n -B 293 35 1 418 99 180 1bba 501 395 458 501 389 63 1shf -A 1 5 13 1 199 1 1ctf 1 1 1 1 1 1 1fc2 501 234 107 501 276 489 1igd 1 1 1 18 10 1 2cro 1 10 1 1 43 16 Total 6 3 8 5 2 4 4state_reduced 4rxn 1 1 8 1 20 26 4pti 1 6 1 1 1 1 1ctf 1 1 1 1 1 1 3icb 3 5 1 5 10 9 1sn3 1 1 1 1 25 3 2cro 1 5 1 1 1 2 1r69 1 4 1 1 1 1 Total 6 3 6 6 4 3 MOULDER 1onc 1 1 1 1 1 1 1dxt 1 1 1 1 3 1 1eaf 1 1 1 1 1 1 1lga 1 1 1 1 1 1 1gky 1 1 1 1 1 1 1cau 1 1 1 1 1 1 4sbv 1 1 1 1 1 1 8i1b 1 1 1 1 1 1 2mta 1 1 1 1 4 4 2fbj 1 1 1 1 1 1 2cmd 1 1 1 1 1 1 1cew 1 1 1 1 1 1 2afn 1 1 1 1 1 1 2sim 1 1 1 1 1 1 1bbh 1 1 1 1 1 1 1mdc 1 1 1 1 1 1 1mup 1 1 1 1 15 1 2pna 85 45 43 85 58 9 1cid 1 1 1 1 1 1 1c2r 1 1 1 1 6 1 Total 19 19 19 19 15 18 Ranking position of the native structure among the sets of model/target decoys for several scoring functions.

Publication Year: 2009


Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins.

(2009) BMC Struct Biol 9

PubMed: 20038291 | PubMedCentral: PMC2809062 | DOI: 10.1186/1472-6807-9-76

The 4-state-reduced decoy data set given in Additional file 1 : Table S1 includes a range of small proteins from 54-75 residues with varying topological folds, with the numbers of decoys ranging from ... 30 for 1ctf to 687 for 4pti .

Publication Year: 2009


A pairwise residue contact area-based mean force potential for discrimination of native protein structure.

(2010) BMC Bioinformatics 11

PubMed: 20064218 | PubMedCentral: PMC2821318 | DOI: 10.1186/1471-2105-11-16

Table 2 Comparison of results with some other residue-based potential function Decoy set Protein DFIRE Rosetta ModPipe Pair ModPipe Surf ModPipe Comb Dope PC2CA Force model TE13 LHL MJ Surfield 4state... reduced 1ctf 1 1 1 1 1 1 1 1 1 1 1 1 1r69 1 2 1 17 1 1 1 8 1 1 1 1 1sn3 1 1 1 7 1 1 1 23 6 1 2 1 2cro 1 5 1 103 1 1 1 4 1 1 1 1 3icb 4 6 15 33 8 1 1 2 - 5 - 1 4pti 1 1 1 71 1 1 1 13 7 1 3 1 4rxn 1 1 1 18 1 1 667 85 16 51 1 1 fisa 1fc2 254 158 491 1 453 357 1 1 - - - 1 1hdd-c 1 90 293 18 135 1 1 1 - - - 1 2cro 1 26 11 146 19 1 1 1 - - - 1 4icb 1 1 196 2 167 1 1 1 - - - 1 lmds 1bba 501 174 501 117 444 501 501 1 - 217 - 1 1fc2 501 291 325 54 222 476 53 1 1 1 1 1 1ctf 1 1 1 1 1 1 1 1 14 500 501 1 1dtk 1 9 4 1 1 1 2 1 5 2 13 1 1igd 1 1 1 3 1 1 1 1 2 9 1 1 1shf-a 1 5 24 18 7 1 1 1 1 17 11 1 2cro 1 2 4 28 12 1 1 1 1 1 1 1 2ovo 1 29 5 8 2 1 1 1 1 3 2 1 4pti 1 4 1 44 1 1 1 1 - 9 - 1 Conclusions The aim of this study was to evaluate a mean force potential based on contact area of residues instead of contact or distance to separate correct from incorrect folds.

Publication Year: 2010


Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.

(2010) PLoS One 5

PubMed: 20463972 | PubMedCentral: PMC2864755 | DOI: 10.1371/journal.pone.0010410

SKIs __________ Chemokines __________ PDZ domains __________ Caspases __________ PDB code Identity PDB code Identity PDB code Identity PDB code Identity 4pti 37.4 1ilq 30.3 1pdr 36.0 1nme 31.0 2knt 42... 2 1plf 31.3 1kwa 22.8 1m72 31.6 1tfx 41.8 1msg 25.6 2fe5 36.3 1pyo 37.5 1aap 42.6 1hum 32.4 1be9 32.5 1i51 32.1 1bik 42.6 1vmp 32.2 1qav 29.7 1qdu 28.7 1dtx 37.3 1rto 40.1 1nte 24.2 1nw9 41.9 1bun 37.1 1dom 26.0 1l6o 31.7 1dem 41.9 1eig 27.9 1qau 30.3 1g2s 26.5 1g9o 35.4 1j9o 18.2 1ihj 28.6 1nr2 38.7 1n7f 30.5 1nap 30.7 2h3l 36.2 1n7e 30.9 1q3o 35.6 2f5y 35.6 2fne 35.2 2byg 36.5 Mean 40.4 30.3 32.3 33.8 a Mean identity of the 8.000 lowest-energy designed sequences relative to each corresponding native template.

Publication Year: 2010


Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.

(2010) BMC Bioinformatics 11

PubMed: 20624289 | PubMedCentral: PMC2912888 | DOI: 10.1186/1471-2105-11-374

1 7.1 1200 8.5 - 17.0  1bg8-A 2.20 1 6.1 1200 6.0 - 15.8  1bl0 2.30 1 6.0 972 3.6 - 18.2  1eh2 NMR 1 4.4 2413 4.0 - 15.3  1jwe NMR 1 8.3 1407 7.8 - 20.9 lattice_ssfit &... x02003;4icb 1.60 1 5.1 1988 4.7 - 12.9  1ctf 1.70 1 6.2 1999 5.4 - 12.8  1fca 1.80 1 4.2 1986 5.1 - 11.4  1pgb 1.92 1 6.2 1997 5.8 - 12.9  1beo 2.20 1 6.6 1998 7.0 - 15.6  1dkt-A 2.90 1 5.5 1995 6.7 - 14.0  1nkl NMR 1 5.2 1995 5.3 - 13.6  1trl-A NMR 1 5.8 1998 5.4 - 12.5 lmds  1igd 1.10 1 8.1 501 3.1 - 12.6  2ovo 1.50 1 5.6 348 4.4 - 13.4  4pti 1.50 1 5.2 344 4.9 - 13.2  1ctf 1.70 1 7.6 496 3.6 - 12.5  1b0n-B 1.90 1 5.3 498 2.4 - 6.0  1shf-A 1.90 1 7.7 437 4.4 - 12.3  2cro 2.35 1 7.7 501 3.9 - 13.5  1fc2 2.80 49 1.5 501 4.0 - 8.4  1bba NMR 501 -3.8 501 2.8 - 8.9  1dtk NMR 3 3.6 216 4.3 - 12.6 Each decoy structure and the native structure were scored and ranked using the Hunter's ScSc term only.

Table 3 Discrimination of native structures in Decoys 'R' Us multiple decoys sets Resolution, Å Rank of native structure Z-score of native structure Number of decoys RMSD range, Å 4state_reduced  1sn3 1.20 1 5.3 660 1.3 - 9.1  4rxn 1.20 1 5.7 677 1.4 - 8.1  4pti 1.50 1 4.4 686 1.4 - 9.3  1ctf 1.70 1 4.7 630 1.3 - 9.1  1r69 2.00 1 6.6 676 0.9 - 8.3  3icb 2.30 15 2.5 654 0.9 - 9.4  2cro 2.35 1 4.1 673 0.8 - 8.3 fisa  4icb 1.60 1 6.6 500 4.8 - 14.1  2cro 2.35 1 5.4 501 4.3 - 12.6  1fc2 2.80 33 1.6 501 3.1 - 10.6  1hdd-C 2.80 1 5.3 501 2.8 - 12.9 fisa_casp3  smd3 ?

Publication Year: 2010


BCL::Score--knowledge based energy potentials for ranking protein models represented by idealized secondary structure elements.

(2012) PLoS One 7

PubMed: 23173051 | PubMedCentral: PMC3500277 | DOI: 10.1371/journal.pone.0049242

set Pdb-Chain DFIRE R osetta ModPipe-Pair ModPipe-Surf ModPipe-Comb DOPE BCL::Score fisa 1fc2 254 158 491 1 453 375 480 fisa 1hdd-C 1 90 293 18 135 1 60 fisa 2cro 1 26 11 146 19 1 1 fisa 4icb 1 1 196 ... 167 1 1 correct 3 1 0 1 (2) 0 3 2 fisa_casp3 1bg8-A 1 1068 1 1180 282 1 9 fisa_casp3 1bl0 1 960 4 912 86 1 246 fisa_casp3 1jwe 1 1177 1 1119 6 1 1 correct 3 0 2 (3) 0 0 (1) 3 1 (2) lmds 1b0n-B 430 300 56 186 18 34 182 lmds 1bba 501 174 501 117 444 501 469 lmds 1fc2 501 291 325 54 222 476 501 lmds 1ctf 1 1 1 1 1 1 12 lmds 1dtk 1 9 4 1 1 1 4 lmds 1igd 1 1 1 3 1 1 1 lmds 1shf-A 1 5 24 18 7 1 2 lmds 2cro 1 2 4 28 12 1 1 lmds 2ovo 1 29 5 8 2 1 1 lmds 4pti 1 4 1 44 1 1 3 correct 7 2 (6) 3 (6) 2 (4) 4 (6) 7 3 (6) lattice_ssfit 1beo 1 1 1 1 1 1 1 lattice_ssfit 1ctf 1 1 1 1 1 1 1 lattice_ssfit 1dtk-A 1 1 1 35 1 1 1 lattice_ssfit 1fca 1 1 1 4 1 1 1 lattice_ssfit 1nkl 1 1 1 1 1 1 1 lattice_ssfit 1pgb 1 1 1 3 1 1 1 lattice_ssfit 1trl-A 1 45 1 123 1 1 6 lattice_ssfit 4icb 1 1 1 3 1 1 1 correct 8 7 8 3 (6) 8 8 7 (8) sum rank 1 21 10 13 6 12 21 13 sum rank 10 21 14 17 12 15 21 18 For different model sets from “decoys‘r’us” [39] , the rank of the native structure, using different energy potentials, was determined.

Publication Year: 2012


A firefly-inspired method for protein structure prediction in lattice models.

(2014) Biomolecules 4

PubMed: 24970205 | PubMedCentral: PMC4030990 | DOI: 10.3390/biom4010056

ID structure length 4RXN mkkytctvcgyiydpedgdpddgvnpgtdfkdipddwvcplcgvgkdefeevee 54 1ENH rprtafsseqlarlkrefnenrylterrrqqlsselglneaqikiwfqnkraki 54 4PTI rpdfcleppytgpckariiryfynakaglcqtfvyggcrakrnnfksae... cmrtcgga 58 2IGD mtpavttyklvingktlkgetttkavdaetaekafkqyandngvdgvwtyddatktftvte 61 2.4.

Publication Year: 2014


The Protein Data Bank archive as an open data resource.

(2014) J Comput Aided Mol Des 28

PubMed: 25062767 | PubMedCentral: PMC4196035 | DOI: 10.1007/s10822-014-9770-y

Early structures included myoglobin ( 1 PDB ID 1mbn [ 6 , 7 ]), the first structure solved by X-ray crystallography, and small enzymes ( 2 top 4pti [ 48 ], bottom right 2cha [ 49 ], bottom left 3cpa [... 50 ]).

Publication Year: 2014


Improved protein structure selection using decoy-dependent discriminatory functions.

(2004) BMC Struct Biol 4

PubMed: 15207004 | PubMedCentral: PMC449718 | DOI: 10.1186/1472-6807-4-8

Protein (PDB code) Number of conformations Empirical function [32] Atomic KBP [8] Shell [33] RAPDF [7] Density score Self-RAPDF 1ctf 630 0.68 0.6 0.65 0.73 0.98 0.89 1r69 675 0.66 0.5 0.52 0.70 0.96 0... 88 1sn3 660 0.53 0.5 0.42 0.47 0.96 0.89 2cro 674 0.58 0.7 0.58 0.76 0.96 0.92 3icb 653 0.77 0.8 0.74 0.85 0.98 0.92 4pti 687 0.46 0.5 0.34 0.49 0.95 0.89 4rxn 677 0.61 0.6 0.57 0.57 0.98 0.88 The density scores and the self-RAPDF scores have the best correlation coefficient with C α RMSDs of decoys relative to experimentally determined conformations for all seven sets.

Publication Year: 2004