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PDB ID Mentions in PubMed Central

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Structural deformation upon protein-protein interaction: a structural alphabet approach.

(2008) BMC Struct Biol 8

PubMed: 18307769 | PubMedCentral: PMC2315654 | DOI: 10.1186/1472-6807-8-12

We consider the 3 classes from Table 3 , namely enzyme/substrate, antibody/antigen, and other; Table 3 Description of the complex set Type (number) Complexes PDB id Enzyme-substrate (23) 1ACB , 1AVX ,... 1AY7 , 1BVN , 1CGI , 1D6R , 1DFJ , 1E6E , 1EAW , 1EWY , 1EZU , 1F34 , 1HIA , 1KKL , 1MAH , 1PPE , 1TMQ , 1UDI , 2MTA , 2PCC , 2SIC , 2SNI , 7CEI Antibody-Antigen (10) 1AHW , 1BGX , 1BVK , 1DQJ , 1E6J , 1JPS , 1MLC , 1VFB , 1WEJ , 2VIS Other (35) 1A2K , 1AK4 , 1AKJ , 1ATN , 1B6C , 1BUH , 1DE4 , 1E96 , 1EER , 1F51 , 1FC2 , 1FQ1 , 1FQJ , 1GCQ , 1GP2 , 1GRN , 1H1V , 1HE1 , 1HE8 , 1I2M , 1I4D , 1IB1 , 1IBR , 1IJK , 1KLU , 1KTZ , 1KXP , 1M10 , 1ML0 , 1N2C , 1QA9 , 1RLB , 1SBB , 1WQ1 , 2BTF • the motif should be located in totality at the protein-protein interfaces of the complexes; • we do not consider runs of helical letters (A,a,V,W,Z,B,C) or extended letters (L,M,N,T,X,J,K).

Publication Year: 2008


Protein-protein docking using region-based 3D Zernike descriptors.

(2009) BMC Bioinformatics 10

PubMed: 20003235 | PubMedCentral: PMC2800122 | DOI: 10.1186/1471-2105-10-407

Original ZDOCK Rank Context Shapes (CS) PatchDock ZDOCK Decoys Reranked by LZerD Score LZerD Complex Rank a) iRMSD HIT2K Rank iRMSD RMSD iRMSD Rank iRMSD HIT2K Rank iRMSD HIT2K 1AHW 268 2.28 21 402 2.... 6 181 2.49 15 1.68 50 5 1.34 42 1AK4 - b) - - - - - - (NA NA NA) 43787 2.35 0 1AKJ 4872 2.29 0 - - - - 1985 1.93 1 - - - 1AVX 2863 2.23 0 - - - - 5689 2.22 0 786 2.41 2 1AY7 5584 1.33 0 - - - - 394 1.1 7 1884 1.98 1 1B6C 1717 2.43 2 - - - - 497 2.13 8 1001 2.41 1 1BJ1 129 0.86 49 1893 1.93 - - 306 1.01 20 298 1.86 7 1BUH 14556 2.37 0 - - - - 11230 2.42 0 12251 1.6 0 1BVK 3970 1.94 0 - - 2754 2.27 9560 2.43 0 5515 2.24 0 1BVN 502 1.97 13 34 2.34 - - 8 2.26 59 27 2.32 6 1CGI 145 2.44 9 - - 1120 2.11 1775 2.14 1 9041 2.1 0 1D6R 2951 2.03 0 - - - - 5022 2.49 0 2619 2.24 0 1DFJ 9 2.27 40 - - - - 9350 2.14 0 - - - 1DQJ 2287 2.48 0 - - - - 5391 2.32 0 20816 2.09 0 1E6E 22643 2.08 0 - - - - 432 1.94 2 52 2.13 8 1E6J 15 1.56 34 - - - - 2509 1.81 0 439 2.18 8 1E96 3094 2.26 0 - - - - 882 1.88 2 216 2.14 2 1EAW 3 1.54 62 94 2.29 85 2.29 5 1.48 111 20 2.42 10 1EWY 259 2.32 2 - - - - 1007 2.14 4 349 2.36 14 1EZU 1100 1.94 3 - - - - 589 1.42 4 824 1.21 2 1F34 5 2.2 13 - - 490 1.81 5082 1.61 0 - - - 1F51 230 2.18 4 - - - - 154 1.76 5 3545 1.58 0 1FQJ 9889 2.29 0 - - - - 628 2.39 2 - - - 1FSK 1 1.63 105 20 1.57 221 2.39 29 1.57 76 15 2.4 11 1GCQ 24339 2.29 0 - - - - 39221 2.29 0 9418 1.8 0 1GHQ - - - - - - - (NA NA NA) 15357 1.68 0 1GRN 1704 2.34 2 - - - - 1884 1.74 1 1407 2.18 1 1HE1 4672 1.31 0 1029 2.17 - - 51 2 8 267 1.98 2 1HIA - - - - - - - (NA NA NA) 44189 2.42 0 1I9R 50 2.45 41 - - - - 57 1.96 10 95 2.39 21 1IJK 52731 2.44 0 - - - - 39460 2.44 0 6731 2.45 0 1IQD 612 2.27 5 - - - - 36 0.99 27 41 1.2 18 1JPS 171 1.81 9 - - - - 5305 1.37 0 292 0.9 20 1K4C 20806 1.53 0 - - - - 4468 1.18 0 1188 1.43 7 1KAC 2896 2.33 0 - - - - 1313 2.33 1 655 2.18 3 1KTZ 53599 1.69 0 - - - - 33926 1.69 0 12162 1.19 0 1KXP 1734 2.36 1 - - - - 32023 1.91 0 14208 2.22 0 1KXQ 212 1.91 13 2226 1.73 - - 629 1.24 4 73 1.68 14 1MAH 92 1.31 9 597 1.16 887 2.28 541 0.89 6 92 0.87 2 1ML0 36 1.56 21 - - 231 2.02 406 1.37 6 559 2.38 3 1MLC 110 1.19 12 18 2.28 - - 243 1.07 12 1834 1.16 1 1NCA 14 1.93 47 - - - - 302 1.55 12 12528 1.5 0 1NSN 185 1.81 5 26 1.79 - - 147 1.81 13 945 2.29 1 1PPE 1 0.57 218 2 2.31 - - 1 0.72 194 1 0.83 68 1QA9 5672 1.88 0 - - - - 5924 1.82 0 1381 2.19 3 1QFW 257 1.14 7 597 1.73 - - 136 2.31 17 108 1.24 4 1RLB - - - - - - - (NA NA NA) 46073 1.24 0 1TMQ 314 1.88 11 783 1.68 1 1.96 90 1.45 19 50 1.45 5 1UDI 258 2.17 4 2649 2.14 27 2.42 219 2.39 3 59 2.36 6 1VFB 2734 1.79 0 228 2.46 - - 1534 1.61 1 1303 1.69 1 1WEJ 465 2.37 8 - - - - 916 1.97 1 3914 2.06 6 1WQ1 1101 2.49 2 - - - - 284 2.05 2 141 1.87 2 2JEL 45 1.79 33 - - - - 149 2.44 19 133 2.49 9 2MTA - - - - - 515 2.19 (NA NA NA) 606 1.64 11 2PCC - - - - - - - (NA NA NA) 4542 2.31 0 2QFW 832 2.29 3 33 2.32 - - 42 1.99 17 68 1.55 29 2SIC 173 1.86 24 1077 2.28 - - 17 1.85 61 12 2.04 9 2SNI 17906 2.44 0 - - - - 428 2.33 2 - - - 7CEI 106 1.97 24 2290 1.9 366 1.07 705 1.57 7 6765 2.03 0 Summary c) ZDOCK CS PatchDock (PD) LZerD Rerank LZerD Rank<100 11 7 3 11 14 Rank<500 26 9 6 26 23 Rank<1000 29 12 9 32 29 Rank<2000 33 15 10 38 36 Wins vs. LZerD Rerank ZDOCK/LZerD Rerank 26/26 CS/LZerD Rerank 5/34 PD/LZerD Rerank 7/34 - - Wins vs. LZerD ZDOCK/LZerD 24/33 CS/LZerD 5/34 PD/LZerD 8/34 LZerD Rerank/LZerD 24/28 - LZerD results are compared with ZDOCK, Context Shapes, and PatchDock.

HEX ZDOCK LZerD Complex Rank lRMSD HITS2K Rank lRMSD HITS2K Rank lRMSD HITS2K 1ACB 694 8.3 3 185 9.98 5 21 9.98 2 1AHW 234 8 3 34 9.86 20 5 2.68 43 1AKJ 209 9.6 10 - - - - - - 1AVX 108 8.9 7 604 9.43 4 - - - 1AY7 645 9.9 4 568 9.39 11 1884 6.13 1 1B6C 593 9 2 182 5.6 10 73 6.2 10 1BUH 743 7.7 2 - - - 599 9.73 1 1BVK - - - 70 7.56 1125 9.83 10 1BVN 63 9.1 20 29 8.65 52 2 6.89 49 1CGI 42 9.4 17 145 3.88 32 86 8.13 12 1D6R 447 7.7 1 303 8.44 3 344 7.84 8 1DE4 946 8.6 1 - - - - - - 1DFJ 17 9.5 14 5 6.64 67 - - - 1DQJ - - - 152 9.82 23 - - - 1E6E 109 5.6 10 - - - 52 4.49 10 1E6J - - - 12 5.34 93 87 9.97 20 1E96 - - - - - - 1375 8.91 1 1EAW 9 5 20 3 5.43 87 6 9.95 19 1EER 609 9.2 8 - - - - - - 1EWY 76 9.1 12 22 8.08 51 103 9.91 110 1EZU - - - - - - 815 7.89 3 1F34 124 6.7 11 5 5.45 20 - - - 1F51 371 9.6 5 602 9.78 4 1101 8.31 1 1FQJ 41 8 12 - - - 1014 9.63 3 1FSK 5 1.8 16 1 4.04 149 15 6.23 28 1GHQ - - - - - - 1571 9.14 1 1GRN 914 9.1 2 1704 5.81 2 1407 7.41 2 1HE1 37 6.4 18 23 8.14 8 47 6.2 7 1HIA 51 8.7 6 - - - 1 9.49 74 1I4D - - - - - - 286 9.11 2 1I9R 82 2.1 8 104 9.07 16 104 9.41 10 1IJK 1012 8.7 3 - - - - - - 1IQD - - - 492 8.99 11 41 6.46 27 1JPS - - - 171 8.51 7 292 2.01 20 1K4C 21 9.6 1 - - - 219 9.78 6 1KAC 687 8.7 1 - - - 655 3.95 3 1KXP 36 9.4 13 1616 7.11 2 1226 8.05 1 1KXQ 488 7.1 5 116 7.58 29 73 4.33 16 1M10 514 9.5 2 - - - - - - 1MAH 2 1.2 20 92 3.86 9 92 2.43 2 1ML0 - - - 36 2.87 35 121 5.71 2 1MLC 408 3.6 2 110 6.17 12 1834 4.48 1 1NCA 116 1.2 5 14 7.08 49 270 9.97 2 1NSN 142 1.5 6 185 5.07 19 94 8.61 4 1PPE 2 9.7 47 1 0.86 358 1 2.26 184 1QA9 - - - - - - 546 8.07 6 1QFW - - - 257 8.63 4 108 9.54 2 1TMQ 356 5.9 9 314 6.12 11 50 3.71 11 1UDI 8 6.2 9 32 8.04 34 19 6.4 16 1VFB - - - 22 8.52 65 150 8.7 22 1WEJ - - - 81 8.36 42 156 9.82 18 1WQ1 125 7.1 10 610 9.9 5 32 9.79 11 2BTF - - - 553 6.39 3 - - - 2JEL 164 6 3 45 4.49 86 66 6.81 35 2MTA 136 9 4 - - - 4 7.57 48 2QFW - - - - - - 68 9.01 11 2SIC 57 8.8 8 173 8.62 18 127 4.59 6 2SNI 256 9.6 7 534 9.69 4 - - - 7CEI 61 8.7 5 106 7.11 28 - - - Summary HEX ZDOCK LZerD Mean 206 173 164 Rank<100 17 19 22 Rank<500 32 33 34 Rank<1000 42 39 38 Rank<2000 43 41 47 Win 18 20 22 The results of HEX are taken from the columns of "U-U shape-only Blind search" in Table 3 of the paper by Ritchie et al .

Publication Year: 2009


Binding-site assessment by virtual fragment screening.

(2010) PLoS One 5

PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109

Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) ACE 1uze 0.60 HIVRT 1vrt 1.66 1o86 0.17 0.37 0.4... 1rt1 1.51 2.45 1.75 1uzf 0.35 0.79 0.69 1c1c a 1.88 3.12 1.61 Alr2 1ah0 1.42 1rth a 1.62 2.28 1.61 1ah3 a 1.06 3.19 1.27 HMGR 1hw8 1.39 2acr a , b 0.88 1.72 1.10 1hwk 0.61 1.49 1.31 CDK2 1aq1 a 1.32 NA 1a4g 0.57 1buh a , b 1.77 3.20 1.44 1a4q a 0.48 2.11 0.52 1dm2 a 1.75 4.49 1.62 1nsc a 0.34 1.49 0.52 COX-2 1cvu 1.51 P38 MAPK 1a9u 1.00 1cx2 a 1.24 3.78 1.53 1kv1 3.84 10.41 1.16 3pgh a 1.11 3.96 1.64 1kv2 3.54 11.26 1.61 DHFR 3dfr 1.01 PDE5 1xoz 1.18 6dfr b 1.47 1.96 1.02 1xp0 0.79 2.23 1.24 ER 1l2i 1.69 PPARg 1fm6 1.46 3ert a 2.61 4.47 1.55 1fm9 a 1.47 4.64 1.62 1err a 2.01 4.39 1.61 2prg a 0.71 1.27 1.43 Fxa 1f0r 1.64 Thrombin 1ba8 1.53 1fjs 1.09 2.57 1.59 1hgt b 0.69 1.85 1.55 1ksn a 0.67 1.65 1.59 TK 1kim a 1.58 1xka a 1.27 2.46 1.56 1ki4 a 1.78 2.90 1.40 RMSD ave was defined as the sidechain RMSD based on binding site residues within a cutoff distance of 4.5 Å from crystallographic ligands; RMSD max is defined as the largest sidechain RMSD value among all the binding site residues.

Publication Year: 2010


Protein docking by Rotation-Based Uniform Sampling (RotBUS) with fast computing of intermolecular contact distance and residue desolvation.

(2010) BMC Bioinformatics 11

PubMed: 20584304 | PubMedCentral: PMC2911459 | DOI: 10.1186/1471-2105-11-352

For instance, there were cases that had poor results with RotBUS (9 Å resolution) filtering at 1% residue-based desolvation, but had good results with FTDock, such as those with PDB code 1ay7 ... 1b6c , 1buh , 1ml0 , 2btf , and 2jel .

Publication Year: 2010


What lessons can be learned from studying the folding of homologous proteins?

(2010) Methods 52

PubMed: 20570731 | PubMedCentral: PMC2965948 | DOI: 10.1016/j.ymeth.2010.06.003

Class (fold) Superfamily Protein (species) Method of investigation PDB code Experimental references Comparative references a All-α (Acyl-CoA binding protein-like) Acyl-CoA binding protein ACBP... (Cow) Φ-Value analysis 2ABD [93,94] [94] ACBP (Rat) WT kinetics 2ABD b [93] ACBP (Yeast) Φ-Value analysis 2ABD b [94] 

 All-α (Acyl carrier protein-like) Colicin E immunity proteins Im7 ( E. coli ) Φ-Value analysis 1AYI [28] [29] Im9 ( E. coli ) Φ-Value analysis 1IMQ [29,30,95] 

 All-α (Cytochrome c ) Cytochrome c Cytochrome c (Horse) Hydrogen exchange 1HRC [96] [97] Cytochrome c 2 ( R. capsulatus ) WT kinetics 1C2R [98] Cytochrome c 551 ( P. aeruginosa ) Minimal Φ-value analysis 2PAC [99] Cytochrome c 552 ( H. thermophilus ) WT kinetics 1AYG [100] Cytochrome c 552 ( T. thermophilus ) WT kinetics 1C52 [101] Mitochondrial cytochrome c (Yeast) WT kinetics 1YCC [102] 

 All-α (Four-helical up-and-down bundle) Cytochromes Cytochrome b 562 ( E. coli ) Hydrogen exchange 1APC [103] FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) FRB (Human) WT kinetics 1AUE [104] 

 All-α (DNA/RNA-binding 3-helical bundle) Homeodomain-like DNA-binding domain of human telomeric protein hTRF1 (Human) WT kinetics 1BA5 [47] [47] En-Hd (Drosophila) Φ-Value analysis 1ENH [7,105] c-Myb DNA-binding domain (Mouse) Φ-Value analysis 1IDY [47] Rap1 (Human) WT kinetics 1FEX [47] 

 All-α (Globin-like) Globin-like Leghemoglobin (Soybean) Hydrogen exchange 1FSL [106] [106] Myoglobin (Sperm whale) Hydrogen exchange 1A6M [107] 

 All-α (peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex) Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex E3 binding domain of dihydrolipoamide acetyltransferase [E3BD] ( B. stearothermophilus ) Φ-Value analysis 1EBD [58] [59] E3-binding domain of dihydrolipoamide succinyltransferase [BBL] ( E. coli ) Φ-Value analysis 1BBL [59] POB ( P. aerophilium ) Φ-Value analysis 1BBL b [60] 

 All-α (ROP-like) ROP protein ROP ( E. agglomerans ) WT kinetics 1ROP b [4] [4] ROP ( E. coli ) WT kinetics 1ROP [4] ROP ( P. vulgaris ) WT kinetics 1ROP b [4] 

 All-α (spectrin repeat-like) Spectrin repeat Alpha chain R15 (Chicken) Φ-Value analysis 1U5P [46] [46] Alpha chain R16 (Chicken) Φ-Value analysis 1CUN [81] Alpha chain R17 (Chicken) Φ-Value analysis 1CUN [45] 

 α/β (α/β knot) α/β knot YbeA ( E. coli ) Φ-Value analysis 1NS5 [108] [108] YibK ( H. influenzae ) Φ-Value analysis 1J85 [109] 

 α/β (Dihydrofolate reductase-like) Dihydrofolate reductase-like Dihydrofolate reductase ( E. coli ) WT kinetics, Ligand binding 1RA9 [110] [110] Dihyrofolate reductase ( L. casei ) WT kinetics, Ligand binding 3DFR [110] Dihydrofolate reductase (Human) WT kinetics, Ligand binding 1KMV [110] 

 α/β (flavodoxin-like) CheY-like CheY ( E. coli ) Φ-Value analysis 1EAY [111] [112] Flavoproteins Apoflavodoxin ( A. vinelandii ) WT kinetics 1YOB [113] Flavodoxin ( Anabaena pcc 7119 ) Φ-Value analysis 1FTG [112] 

 α/β (Phosphoglycerate kinase) Phosphoglycerate kinase Phosphoglycerate kinase ( B. stearothermophilus ) Minimal Φ-value analysis 1PHP [114] Phosphoglycerate kinase (Yeast) WT kinetics 3PGK [115] 

 α/β (RNase-H-like Motif) RNase-H-like RNase-H ( E.coli ) Hydrogen exchange Limited mutagenesis 1F21 [168,169] RNase-H ( T. thermophilus ) Hydrogen exchange 1RIL [170] [170,171] RNase-H ( C. tepidum ) WT kinetics 3H08 [171] 

 α/β (TIM β/α-barrel) Ribulose-phosphate binding barrel Trptophan synthase α-subunit [αTS] ( E. coli ) WT kinetics 1V7Y [116] [117] Indole-3-glycerophosphate synthase [sIGPS] ( S. solfataricus ) WT kinetics, Hydrogen exchange 1IGS [118,119] 

 Xylose isomerase-like IOLI ( B. subtilis ) WT kinetics 1I60 [117] 

 α + β (Ferredoxin-like) Acyl-phosphatase-like AcP (Human) Φ-Value analysis 1APS b [26,120] [26,65,121] HypF ( E. coli ) WT kinetics 1GXU [121] Protease propeptides/inhibitors Procarboxy-peptidase A2 (Human) Φ-Value analysis 1O6X [27] Ribosomal protein S6 S6 ( A. aeolicus ) Φ-Value analysis 2J5A [65] S6 ( T. thermophilus ) Φ-Value analysis 1RIS [69] RNA binding domain (RBD) U1A (Human) Φ-Value analysis 1FHT [13] 

 α + β (β-hairpin-α-hairpin repeat) Ankyrin repeat AnkyrinR D34 (Human) Minimal Φ-value analysis 1N11 [122] [123] Ankyrin repeats in tumor suppressor p16 (Human) Φ-Value analysis 1BI7 [52] Cell-cycle inhibitor p19ink4D (Human) WT kinetics 1BD8 [124] Myotrophin (Rat) Φ-Value analysis 2MYO [51] Neurogenic locus notch receptor domain (Drosophila) Minimal Φ-value analysis, WT redesign 1OT8 [125,126] 

 α + β (Cell-cycle regulatory proteins) Cell-cycle regulatory proteins CksHs1 (Human) Φ-Value analysis 1BUH [70] [70] CksHs2 (Human) WT kinetics 1CKS [127] Suc1 ( S. pombe ) Φ-Value analysis 1PUC [128] 

 α + β (Lysozyme-like) Lysozyme-like Lysozyme (Hen Egg White) WT kinetics 1E8L [129] [130] α-Lactalbumin (Bovine) WT kinetics 1F6S [130] α-Lactalbumin (Goat) Minimal Φ-value analysis, Hydrogen exchange 1HFY [131,132] [131] Milk lysozyme (Dog) Hydrogen exchange 1EL1 [131,133] 

 α + β (β-grasp: ubiquitin-like) Immunoglobulin-binding domains Protein G ( Streptococcus ) Φ-Value analysis 2IGD [42] [42,134,135] Immunoglobulin light chain-binding domain of Protein L ( P. magnus ) Φ-Value analysis 2PTL [41] Ubiquitin-like c-Raf1 RBD (Human) Φ-Value analysis 1RFA [134,135] Ubiquitin (Human) Minimal Φ-value analysis 1UBQ [136] Ubiquitin (Yeast) Φ-Value analysis 1Q0W [137] 

 All-β (Ig-like β-sandwich) Fibronectin type III CAfn2 ( B. circulans ) Φ-Value analysis 1K85 [19] [15,19] FnIII-9 (Human) WT kinetics 1FNF [138] FnIII-10 (Human) Φ-Value analysis 1FNF [16] TNfn3 (Human) Φ-Value analysis 1TEN [18] Immunoglobulin TI I27 (Human) Φ-Value analysis 1TIT [17] CD2 (Rat) Minimal Φ-value analysis 1HNG [37] Various antibody domains (V L , C L , C H 2, C H 3) WT kinetics [139–142] [142] 

 All-β (Lipocalins) Lipocalins CRABP I (Mouse) WT kinetics 2CBR [143,144] [32,143] CRBP II (Rat) WT kinetics 1OPA [143] IFABP (Rat) Minimal Φ-value analysis 1IFC [31,32,143,145] ILBP (Rat) Minimal Φ-value analysis 1O1V b [31,32] 

 All-β (OB-fold) Nucleic acid-binding proteins Bc-Csp ( B. caldolyticus ) Φ-Value analysis 1C9O [146,147] [146,148] CspA ( E. coli ) Hydrogen exchange 1MJC [149] Bs-CspB ( B. subtilis ) Φ-Value analysis 1CSP [150] Tm-Csp ( T. maritima ) WT kinetics 1G6P [148] 

 All-β (PDZ domain-like) PDZ domain-like PDZ2 domain from PTP-BL (Mouse) Φ-Value analysis 1GM1 [57] [151] Third PDZ domain from synaptic protein PSD-95 (Rat) Hydrogen exchange Φ-value analysis 1BE9 [151,152] 

 All-β (SH3-like barrel) Chromo domain-like DNA-binding protein Sso7d ( S. solfataricus ) Φ-Value analysis 1SSO [153] [21,153] SH3-domain α-Spectrin SH3-domain (Chicken) Φ-Value analysis, WT redesign 1SHG [22,154] Fyn proto-oncogene tyrosine kinase SH3-domain (Chicken) Φ-Value analysis, NMR dispersion 1FYN b [23,24,155,156] Actin binding protein ABP1 (Yeast) NMR dispersion 1JO8 [21] Phosphatidylinositol 3-kinase SH3-domain (Cow) WT kinetics 2PNI [157] c-src protein tyrosine kinase (Chicken) Φ-Value analysis 1SRM [25] 

 All-β (WW domain-like) WW domain Formin Binding Protein 28 (Mouse) Φ-Value analysis 1E0L [8,158]   Mitotic rotamase PIN1 (Human) Φ-Value analysis 1PIN [48,159] Yap65 WW domain (Human) WT kinetics 1JMQ [160] 

 Coiled coil proteins (Parallel coiled-coil) Leucine zipper domain GCN4 (Yeast) WT kinetics, Minimal Φ-value analysis 2BNI [161,162] c-Jun (Human) Dimer thermodynamics 1JUN [163] c-Fos (Human) Dimer thermodynamics 1FOS [163] a Comparative references are those in which the folding mechanisms/pathways of homologous proteins are compared and discussed.

Publication Year: 2010


Designing coarse grained-and atom based-potentials for protein-protein docking.

(2010) BMC Struct Biol 10

PubMed: 21078143 | PubMedCentral: PMC2996388 | DOI: 10.1186/1472-6807-10-40

Table 5 Ranking ZDOCK2.3 decoys (IRMSD ≤2.5Å) by the jackknife test Complex Rank a ADPs-II b Zdock2.3 1B6C 311 168 1BVK - - 1DQJ - - 1EWY 754 113 1IJK 1131 - 1AVX 955 449 1D6R - - 1E96... 326 399 1F34 - 26 1GCQ - - 1GRN 492 807 1KXP 381 7 1NSN - 445 1SBB - - 1AKJ - 96 1AY7 236 - 1DFJ 720 1 1EAW 152 13 1I9R 329 90 1UDI 386 13 2PCC - - 1AHW 23 56 1BUH 16 - 1E6E 2 103 1ML0 10 1 1PPE 3 1 1QFW 1080 74 1TMQ 9 126 1WEJ 3 102 2JEL 307 86 7CEI 42 1 1BJ1 6 18 1CGI - - 1F51 1 11 1KAC - 1523 1NCA 4 4 1QA9 - - 2SNI 17 - 1RLB 48 302 Top10 8 (20.5%) 6 (15.4%) a-Rank of the lowest energy near-native decoy with IRMSD ≤2.5Å out of 54000 predictions.

Table 4 Ranking ZDOCK2.3 decoys (IRMSD ≤4Å) by the jackknife test Complex a Rank b ADPs-II c Zdock2.3 DARS ACE 1AK4 - - 950 1744 1B6C 95 16 9 178 1BVK 12 268 610 - 1DQJ - 1490 - - 1EWY 164 18 42 364 1FC2 484 - 24 797 1GHQ - - - 1308 1HIA 21 653 122 - 1IJK 1131 - 368 - 1KLU - - - - 1AVX 5 46 6 59 1D6R 1840 567 - - 1E96 39 399 42 490 1F34 13 26 666 5 1GCQ 1030 - 1057 1040 1GRN 210 102 - - 1I4D 84 403 965 616 1KXP 91 7 1 200 1NSN 53 445 - - 1SBB - - - - 1ACB 113 55 24 98 1AKJ 592 40 - - 1AY7 120 100 - - 1DFJ 37 1 - - 1EAW 65 13 33 309 1FQ1 - - - - 1GP2 4 389 58 1681 1I9R 184 14 589 - 1UDI 27 13 1 1 2PCC 203 193 821 120 1AHW 23 14 - - 1BUH 14 - 555 - 1E6E 2 103 44 520 1ML0 10 1 9 32 1PPE 3 1 1 1 1QFW 544 74 - - 1TMQ 9 126 12 22 1WEJ 3 42 1047 - 2JEL 307 86 76 579 7CEI 15 1 920 708 1ATN - - - - 1BJ1 6 18 18 85 1CGI 71 247 13 24 1F51 1 11 251 797 1KAC 121 1389 - - 1KKL 283 - 1 222 1NCA 4 4 - - 1QA9 687 - - - 2SNI 17 618 1 2 1RLB 48 302 5 7 a-Complex PDB code.

Publication Year: 2010


Sampling the conformation of protein surface residues for flexible protein docking.

(2010) BMC Bioinformatics 11

PubMed: 21092317 | PubMedCentral: PMC3002368 | DOI: 10.1186/1471-2105-11-575

Table 1 The different docking test cases included in our experiments Complex PDB ID 1ACB 1AHW 1AK4 1AKJ 1AY7 1B6C 1BJ1 1BKD 1BUH 1BVK 1BVN 1CGI 1D6R 1DFJ 1DQJ 1E6E 1E6J 1EAW 1EER 1EWY 1FC2 1FSK 1GHQ 1... 9R 1IBR 1IQD 1KAC 1KTZ 1KXQ 1M10 1MAH 1ML0 1MLC 1NCA 1NSN 1QFW 1R0R 1S1Q 1SBB 1TMQ 1UDI 1VFB 1WEJ 1WQ1 1Y64 2AJF 2B42 2FD6 2I25 2JEL 2MTA 2QFW a 2SIC 2UUY 2VIS 7CEI a Note that the name 2QFW does not correspond to the actual PDB file with this ID.

Publication Year: 2010


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ(N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd CAPRI quality 1OPH rigid-body | E... 5 5.0 [0.0] 1.00 0.23 *** 1YVB rigid-body | E 4 4.0 [0.9] 0.71 1.32 ** 1ML0 rigid-body | O 5 5.0 [0.0] 1.00 0.40 *** 1ZHI rigid-body | O 4 4.0 [0.9] 0.72 1.47 ** 1KTZ rigid-body | O 5 5.0 [0.0] 1.00 0.51 *** 1XQS medium | O 4 3.9 [1.0] 0.70 1.47 ** 1PPE rigid-body | E 5 5.0 [0.0] 1.00 0.91 *** 2OOB rigid-body | O 4 3.9 [1.2] 0.69 1.04 ** 1B6C rigid-body | O 5 5.0 [0.0] 1.00 1.51 ** 1DFJ rigid-body | E 4 3.6 [1.4] 0.57 1.39 ** 2HLE rigid-body | O 5 5.0 [0.2] 1.00 0.89 *** 1BJ1 rigid-body | AB 4 3.6 [1.2] 0.57 2.25 * 1KXP rigid-body | O 5 5.0 [0.2] 1.00 1.16 ** 2CFH medium | O 4 3.6 [1.1] 0.56 1.25 ** 2HRK medium | O 5 5.0 [0.2] 0.99 1.42 ** 1BVK rigid-body | A 3 3.5 [1.2] 0.51 1.77 ** 1QA9 rigid-body | O 5 5.0 [0.1] 1.00 0.59 *** 1AVX rigid-body | E 3 3.4 [1.1] 0.50 1.87 ** 1FSK rigid-body | AB 5 5.0 [0.1] 1.00 1.03 ** 1MAH rigid-body | E 3 3.4 [1.1] 0.50 1.94 ** 1JPS rigid-body | A 5 4.9 [0.5] 0.97 1.15 ** 1VFB rigid-body | A 4 3.4 [1.1] 0.50 1.96 ** 1AK4 rigid-body | O 5 4.9 [0.5] 0.97 1.36 ** 2SNI rigid-body | E 3 3.3 [1.1] 0.47 1.14 ** 1UDI rigid-body | E 5 4.9 [0.4] 0.98 2.17 * 1KXQ rigid-body | AB 3 3.3 [1.1] 0.44 1.25 ** 1D6R rigid-body | E 5 4.9 [0.3] 0.99 2.14 * 1BUH rigid-body | O 3 3.3 [1.1] 0.44 1.73 ** 7CEI rigid-body | E 5 4.8 [0.6] 0.94 0.79 *** 1XD3 rigid-body | O 3 3.3 [1.1] 0.45 2.69 * 2UUY rigid-body | E 5 4.7 [0.7] 0.93 1.30 ** 1E4K difficult | A 4 3.2 [1.3] 0.45 1.98 ** 1E6E rigid-body | E 5 4.7 [0.6] 0.94 0.79 *** 1E6J rigid-body | A 3 3.2 [1.2] 0.40 2.48 * 1SBB rigid-body | O 5 4.6 [0.7] 0.91 0.60 *** 1HIA rigid-body | E 3 3.2 [1.1] 0.40 1.95 ** 2C0L difficult | O 5 4.6 [0.7] 0.91 1.15 ** 2SIC rigid-body | E 3 3.1 [1.3] 0.40 0.59 *** 1IQD rigid-body | AB 5 4.5 [0.8] 0.89 1.26 ** 2FD6 rigid-body | A 3 3.1 [1.2] 0.38 1.85 ** 1AHW rigid-body | A 5 4.5 [0.7] 0.89 1.38 ** 1HE1 rigid-body | O 3 3.0 [1.2] 0.36 1.31 ** 1GCQ rigid-body | O 5 4.4 [0.8] 0.88 0.72 *** 2JEL rigid-body | AB 3 3.0 [1.1] 0.36 0.40 *** 1EAW rigid-body | E 4 4.4 [0.8] 0.87 1.31 ** 1AY7 rigid-body | E 3 2.9 [1.1] 0.32 1.55 ** 1FC2 rigid-body | O 4 4.4 [0.8] 0.84 1.53 ** 1WQ1 medium | O 3 2.8 [1.3] 0.30 1.48 ** 1GPW rigid-body | O 4 4.4 [0.8] 0.88 1.98 ** 2QFW rigid-body | AB 3 2.8 [1.2] 0.30 0.64 *** 2MTA rigid-body | E 4 4.3 [0.9] 0.81 0.66 *** 1IJK medium | E 3 2.8 [1.2] 0.28 2.35 * 1BVN rigid-body | E 4 4.0 [1.0] 0.72 1.35 ** 1NCA rigid-body | AB 3 2.7 [1.3] 0.27 0.46 *** 1CGI rigid-body | E 4 4.0 [1.0] 0.74 1.76 ** 2I25 rigid-body | A 3 2.2 [1.2] 0.15 1.80 ** 10.1371/journal.pone.0022477.

Publication Year: 2011


Prediction of protein-binding areas by small-world residue networks and application to docking.

(2011) BMC Bioinformatics 12

PubMed: 21943333 | PubMedCentral: PMC3189935 | DOI: 10.1186/1471-2105-12-378

(C) Ligand of the "other" type complex between CDK2 kinase and the human cyclin dependent kinase subunit (PDB code 1BUH ), in which all four predicted residues are in the binding site.

Publication Year: 2011


Protein docking prediction using predicted protein-protein interface.

(2012) BMC Bioinformatics 13

PubMed: 22233443 | PubMedCentral: PMC3287255 | DOI: 10.1186/1471-2105-13-7

First example is human cdk2 kinase complex with cell cycle-regulatory protein ckshs1 (PDB ID: 1BUH ).

Publication Year: 2012


Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

(2013) PLoS One 8

PubMed: 23874954 | PubMedCentral: PMC3712918 | DOI: 10.1371/journal.pone.0069365

Rigid-body (34) 1AK4 1AVX 1AY7 1B6C 1BUH 1BVN 1CGI 1D6R 1DFJ 1E6E 1E96 1EAW 1EWY 1F34 1FC2 1FQJ 1GCQ 1GHQ 1HE1 1KAC 1KTZ 1KXP 1KXQ 1MAH 1PPE 1QA9 1SBB 1TMQ 1UDI 2BTF 2PCC 2SIC 2SNI 7CEI Medium Difficu... ty (6) 1ACB 1GRN 1HE8 1I2M 1M10 1WQ1 Difficult (4) 1ATN 1FQ1 1H1V 1IBR Definition of IFP and Similarity between Decoys As suggested previously, it is sufficient to compare the interacting fragments rather than the whole structures to obtain information on near-native molecular interactions [9] , [10] .

Publication Year: 2013


Multisite phosphorylation networks as signal processors for Cdk1.

(2013) Nat Struct Mol Biol 20

PubMed: 24186061 | PubMedCentral: PMC3855452 | DOI: 10.1038/nsmb.2706

The model was created by superimposing domains from crystal structures (PDB codes: 1BUH, 2CCI, 4LPA) solved in the presence of the relevant substrate peptide bound to the pocket 41 , 45 , 55 .

Publication Year: 2013


Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

(2014) PLoS Comput Biol 10

PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741

Target Structural data Docking-based druggability Protein flexibility Variation PDB ID RMSD ave (Å) [A] dock hit rate [B] DScore+ [A] [B] CDK2 1aq1 1.32 1.7 21% 11% 1buh 1.8 1.44 1.7 1dm2 1.8 ... .62 1.9 ER 1l2i 1.69 2.9 9% 7% 3ert 2.6 1.55 2.7 1err 2.0 1.61 2.8 HIV RT 1vrt 1.66 2.5 8% 13% 1rt1 1.5 1.75 2.3 1c1c 1.9 1.61 2.2 1rth 1.6 1.61 2.3 p38α 1a9u 1.00 1.8 49% 15% kinase 1kv1 3.8 1.16 2.1 1kv2 3.5 1.61 2.1 PPARγ 1fm6 1.46 2.9 13% 34% 1fm9 1.5 1.62 3.0 2prg 0.7 1.43 2.1 TK 1kim 1.58 2.7 12% 4% 1ki4 1.8 1.40 2.6 IL-2 1z92 0.13 * 107% 13% 1py2 2.6 0.62 * 1m48 2.5 0.62 * Bcl-XL 2bzw 1.04 2.4 21% 4% 2yxj 2.5 0.84 2.5 TNF 1tnf 0.95 2.4 1% 18% 2az5 2.9 0.96 2.0 MDM2 1ycr 0.45 2.5 69% 18% 1rv1 1.8 0.92 2.2 1t4e 1.6 0.66 2.1 HPV E2 1tue -0.24 * 323% 31% 1r6n 2.8 1.02 * Targets are from Huang and Jacobson [17] , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.

Publication Year: 2014


Physicochemical mechanisms of protein regulation by phosphorylation.

(2014) Front Genet 5

PubMed: 25147561 | PubMedCentral: PMC4124799 | DOI: 10.3389/fgene.2014.00270

(B) A model of the cyclin–Cdk–Cks1 complex with the relevant substrate peptide constructed based on 1BUH, 2CCI, and 4LPA PDB structures [as described in the previous paper ( Koivomagi ... t al., 2013 )].

Publication Year: 2014


Protein-protein docking with dynamic residue protonation states.

(2014) PLoS Comput Biol 10

PubMed: 25501663 | PubMedCentral: PMC4263365 | DOI: 10.1371/journal.pcbi.1004018

For example, the CDK2 kinase–cell cycle-regulatory protein CksHs1 complex (1BUH; pH 7.5 [41] ) has four native hydrogen bonds.

Docking plots generated using RosettaDock and pHDock for (A) tumor susceptibility gene 101 protein–Ubiquitin complex (1S1Q; pH 4.6), (B) PPARgamma+RXRalpha–GW409544+co-activator peptide complex (1K74; pH 7.5), and (C) CDK2 kinase–cell cycle-regulatory protein CksHs1 complex (1BUH; pH 7.5).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4443796

Rigid-body (34) 1AK4, 1AVX, 1AY7, 1B6C, 1BUH, 1BVN, 1CGI, 1D6R, 1DFJ, 1E6E, 1E96, 1EAW, 1EWY, 1F34, 1FC2, 1FQJ, 1GCQ, 1GHQ, 1HE1, 1KAC, 1KTZ, 1KXP, 1KXQ, 1MAH, 1PPE, 1QA9, 1SBB, 1TMQ, 1UDI, 2BTF, 2PCC... 2SIC, 2SNI, 7CEI Medium Difficulty (6) 1ACB, 1GRN, 1HE8, 1I2M, 1M10, 1WQ1 Difficult (4) 1ATN, 1FQ1, 1H1V, 1IBR Table 4 The 120 complex structures selected from the ZLAB Benchmark 4.0 dataset (large dataset).

Publication Year: 2014