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Protein subunit interfaces: heterodimers versus homodimers.

(2005) Bioinformation 1

PubMed: 17597849 | PubMedCentral: PMC1891636 | DOI: null

References 1 Jones S Thornton JM Proc Natl Acad Sci 1996 93 13 8552589 2 Xu D Protein Engineering 1997 10 999 9464564 3 Tsai CJ Protein Science 1997 6 53 9007976 4 Conte L Lo J Mol Biol 1999 285 2177 ... 925793 5 Chakrabarti P Janin J Proteins 2002 47 334 11948787 6 Brinda KV Protein Eng 2002 15 265 11983927 7 Bahadur RP Proteins 2003 53 708 14579361 8 Nooren IM Thornton JM J Mol Biol 2003 325 991 12527304 9 Caffrey DR Protein Sci 2004 13 190 14691234 10 Zhanhua C Frontiers in Bioscience 2005 10 844 15569623 11 Jones S Thornton JM Prog Biophys Mol Biol 1995 63 31 7746868 12 Lijnzaad P Argos P Proteins 1997 28 333 9223180 13 Dasgupta S Proteins 1997 28 494 9261866 14 Valdar WS Thornton JM J Mol Biol 2001 313 399 11800565 15 Li L Frontiers in Bioscience 2005 10 1977 15769678 16 Lee B Richard EM J Mol Biol 1971 55 379 5551392 17 Rodriguez R Bioinformatics 1998 14 523 9694991 18 Jones S Thornton JM J Mol Biol 1997 272 121 9299342 Figures and Tables Table 1 Dataset Creation Hetero-dimers PDB code Resolution n (Å) Chain one Name of chain one Length Chain two Name of chain two Length 1YCS 2.2 B 53BP2 193 A P53 191 1ABR 2.1 B Abrin-A 267 A Carbohydrate 251 1KU6 2.5 A Acetylcholinesterase 535 B Fasciculin 2 61 1LFD 2.1 B Active ras protein 167 A Ras-interacting domain of ralgds 87 1JIW 1.7 P Alkaline metalloproteinase 470 I Proteinase inhibitor 105 1BPL 2.2 B Alpha-amylase 290 A Alpha-amylase 179 1KXV 1.6 A Alpha-amylase 496 C Camelid VHH domain cab10 119 1TMQ 2.5 A Alpha-amylase 470 B Ragi bifunctional inhibitor 117 1BVN 2.5 P Alpha-amylase 496 T Tendamistat 71 1ACB 2.0 E Alpha-chymotrypsin 241 I Eglin C 63 1CHO 1.8 E Alpha-chymotrypsin 238 I Turkey ovomucoid third domain 53 1CGI 2.3 E Alpha-chymotrypsinogen 245 I Trypsin inhibitor 56 1SLU 1.8 B Anionic trypsin 216 A Ecotin 131 1RE0 2.4 B ARF guanine-nucleotide exchange factor 1 195 A ADP-ribosylation factor 1 162 1KSH 1.8 A ARF-like protein 2 164 B Cyclic phosphodiesterase delta-subunit 141 1MG9 2.3 B ATP dependent CLP protease 143 A Protein YLJA 84 1BRL 2.4 A Bacterial luciferase 340 B Bacterial luciferase 319 1AVA 1.9 A Barley alpha-amylase 2 403 C Barley alpha-amylase/subtilisin inhibitor 181 1B27 2.1 A Barnase 110 D Barstar 90 1LUJ 2.5 A Beta-catenin 501 B Beta-catenin-interacting protein ICAT 71 1S0W 2.3 A Beta-lactamase tem 263 C Beta-lactamase inhibitory protein 165 1BND 2.3 A Brain derived neurotrophic factor 109 B Neurotrophin 3 108 1D4X 1.8 A C. Elegans actin 1/3 368 G Gelsolin 124 1G4Y 1.6 R Calmodulin 147 B Calcium-activated potassium channel RSK2 81 1DTD 1.7 A Carboxypeptidase A2 303 B Metallocarboxypeptidase inhibitor 61 1NW9 2.4 B Catalytic domain of caspase-9 238 A Inhibitor of apoptosis protein 3 91 1OKK 2.1 D Cell division protein 265 A Signal recognition particle protein 290 1H1S 2.0 A Cell division protein kinase 2 296 B Cyclin A2 258 1OHZ 2.2 A Cellulosomal scaffolding protein A 140 B Endo-1 4-beta-xylanase Y 56 1HL6 2.5 A CG8781 protein 119 B Mago nashi protein 137 1P5V 1.7 A Chaperone protein CAF1M 191 B F1 capsule antigen 136 1PDK 2.4 A Chaperone protein PAPD 296 B Protein PAPK 258 1N0L 2.3 A Chaperone protein PAPD 212 B Mature fimbrial protein PAPE 116 1FFG 2.1 B Chemotaxis protein chea 68 A Chemotaxis protein chey 128 1EAY 2 A Chey 128 C Chea 67 1P2M 1.8 A Chymotrypsinogen A 238 B Pancreatic trypsin inhibitor 58 1HCG 2.2 A Coagulation factor 236 B Coagulation factor 51 1V74 2.0 A Colicin D 107 B Colicin D immunity protein 87 1E44 2.4 B Colicin E3 96 A Immunity protein 84 1FR2 1.6 B Colicin E9 131 A Colicin E9 immunity protein 83 1F5Q 2.5 A Cyclin dependent kinase 2 296 B Gamma herpesvirus cyclin 247 1FIN 2.3 A Cyclin-dependent kinase 298 B Cyclin A 260 1BLX 1.9 A Cyclin-dependent kinase 6 305 B P19ink4D 160 1M9E 1.7 A Cyclophilin A 164 D HIV-1 capsid 135 1S6V 1.9 A Cytochrome C peroxidase 294 B Cytochrome C 108 1R8S 1.5 E Cytohesin 2 187 A ADP-ribosylation factor 1 160 1UJZ 2.1 B Designed colicin E7 dnase 127 A Designed colicin E7 immunity protein 87 1NLV 1.8 A Dictyostelium discoideum actin 364 G Gelsolin 123 1H31 1.5 A Diheme cytochrome C 260 B Cytochrome C 138 1EM8 2.1 A DNA polymerase III CHI subunit 147 B DNA polymerase III PSI subunit 110 1JQL 2.5 A DNA polymerase III beta chain 366 B DNA polymerase III delta subunit 140 1EAI 2.4 A Elastase 240 C Chymotrypsin isoinhibitor 1 61 1EFV 2.1 A Electron transfer flavoprotein alpha chain 312 B Electron transfer flavoprotein beta chain 252 1F60 1.7 A Elongation factor EEF1A 440 B Elongation factor EEF1BA 90 1TA3 1.7 B Endo-1 4-beta-xylanase 301 A Xylanase inhibitor protein I 274 1TE1 2.5 B Endo-1 4-xylanase 190 A Xylanase inhibitor protein I 274 3FAP 1.9 A FK506-binding protein 107 B FKBP12-rapamycin associated protein 94 1FCD 2.5 A Flavocytochrome C sulfide dehydrogenase 401 C Flavocytochrome c sulfide dehydrogenase 174 1NF3 2.1 A G25k GTP-binding protein 194 C PAR-6B 123 1NQI 2 B Galactosyltransferase 272 A Alpha lactalbumin 123 1WQ1 2.5 G Gapette 320 R Harvey-RAS 166 1OR0 2.0 B Glutaryl acylase beat subunit 510 A Glutaryl acylase alpha subunit 152 1AXI 2.1 B Growth hormone receptor 191 A Growth hormone 175 2NGR 1.9 B Gtpase activating protein 196 A GTP binding protein 191 1TX4 1.7 A Gtpase-activating protein rhogap 196 B Transforming protein RHOA 174 1AY7 1.7 A Guanyl-specific ribonuclease SA 96 B Barstar 89 1HX1 1.9 A Heat shock cognate 71 KDA 377 B Bag-family molecular chaperone regulator-1 112 1USU 2.2 A Heat shock protein HSP82 246 B AHA1 132 2HBE 2.0 B Hemoglobin 146 A Hemoglobin 141 1GPW 2.4 A Hisf protein 253 B Amidotransferase HISF 200 1CXZ 2.2 A His-tagged transforming protein RHOA 182 B PKN 86 1US7 2.3 B HSP90 chaperone protein kinase 194 A Heat shock protein HSP82 207 1KXP 2.1 D Human vitamin D-binding protein 438 A Actin alpha skeletal muscle 349 1H2A 1.8 L Hydrogenase 534 S Hydrogenase 267 1KA9 2.3 F Imidazole glycerol phosphtate synthase 251 H Imidazole glycerol phosphtate synthase 195 1IBR 2.3 B Importin beta-1 subunit 458 A GTP-binding nuclear protein ran 169 1PVH 2.5 A Interleukin 6 signal transducer 201 B Leukemia inhibitory factor 169 1IAR 2.3 B Interleukin-4 receptor alpha chain 188 A Interleukin 129 1I1R 2.4 A Interleukin-6 receptor beta chain 301 B Viral IL-6 167 1O6S 1.8 A Internalin A 461 B E-cadherin 105 1KI1 2.3 B Intersectin long form 342 A G25k GTP-binding protein 178 2KIN 1.9 A Kinesin 238 B Kinesin 100 1PPF 1.8 E Leukocyte elastase 218 I Ovomucoid inhibitor 56 1OP9 1.9 B Lysozyme C 130 A Hl6 camel VHH fragment 121 1UUZ 1.8 D Lysozyme C 129 A Inhibitor of vertebrate lysozyme 130 1OO0 1.9 A Mago nashi protein 144 B Drosophila Y14 92 1SVX 2.2 B Maltose-binding periplasmic protein 369 A Ankyrin repeat protein OFF7 157 1PQZ 2.1 A MCMV M144 238 B Beta-2-microglobulin 99 1MEE 2.0 A Mesentericopeptidase 275 I Eglin-C 64 1JW9 1.7 B Molybdopterin biosynthesis moeb protein 240 D Molybdopterin converting factor 81 1Q40 2.0 B Mrna export factor MEX67 180 A Mrna transport regulator MTR2 163 1SHW 2.2 B Neural kinase 181 A Ephrin-A5 138 1QAV 1.9 B Neuronal nitric oxide synthase 115 A Alpha-1 syntrophin 90 1E96 2.4 B Neutrophil cytosol factor 2 185 A Ras-related C3 botulinum toxin substrate 1 178 1NPE 2.3 A Nidogen 263 B Laminin gamma-1 chain 164 1GL4 2.0 A Nidogen-1 273 B Proteoglycan core protein 89 1M4U 2.4 A Noggin 199 L Osteogenic protein 1 112 1FYH 2.0 A Nterferon-gamma 242 B Interferon-gamma receptor alpha chain 201 1STF 2.4 E Papain 212 I Stefin B 98 1F34 2.5 A Pepsin A 325 B Major pepsin inhibitor PI-3 138 1UBK 1.2 L Periplasmic hydrogenase large subunit 534 S Periplasmic hydrogenase small subunit 267 1JLT 1.4 B Phospholipase A2 122 A Phospholipase A2 inhibitor 122 1L4Z 2.3 A Plasminogen 248 B Streptokinase 125 1DHK 1.9 A Porcine pancreatic alpha-amylase 495 B Bean lectin-like inhibitor 195 3YGS 2.5 P Procaspase 9 97 C Apoptotic protease activating factor 1 95 1FT1 2.3 B Protein farnesyltransferase 416 A Protein farnesyltransferase 315 1G4U 2.3 S Protein tyrosine phosphatase SPTP 360 R Ras-related C3 botulinum toxin substrate 1 180 1CT4 1.6 E Proteinase 185 I Ovomucoid inhibitor 51 1VG0 2.2 A Rab escort protein 1 481 B Ras-related protein rab-7 182 1F2T 1.6 A Rad50 abc-atpase N-terminal domain 145 B Rad50 abc-atpase C-terminal domain 143 1GUA 2.0 A Rap1A 167 B C-raf1 76 1HE1 2.0 C Ras-related C3 botulinum toxin substrate 1 176 A Exoenzyme S 135 1DS6 2.4 A Ras-related C3 botulinum toxin substrate 2 181 B RHO GDP-dissociation inhibitor 2 179 1C1Y 1.9 A Ras-related protein 167 B Proto-onkogene serine 77 1DFJ 2.5 E Ribonuclease A 124 I Ribonuclease inhibitor 456 1DZB 2.0 A SCFV fragment 1F9 224 X Turkey egg-white lysozyme C 129 1H2S 1.9 A Sensory rhodopsin II 225 B Sensory rhodopsin II transducer 60 1P57 1.8 B Serine protease hepsin heavy chain 247 A Serine protease hepsin light chain 110 4SGB 2.1 E Serine proteinase B 185 I Potato inhibitor 51 1SMP 2.3 A Serratia metallo proteinase 468 I Erwinia chrysanthemi inhibitor 100 1NRJ 1.7 B Signal recognition particle receptor 191 A Docking protein 147 1RJ9 1.9 A Signal recognition protein 277 B Signal recognition particle protein 282 1JTP 1.9 A Single-domain antibody 135 L Lysozyme C 129 1SGD 1.8 E Streptogrisin B 185 I Ovomucoid 51 1LW6 1.5 E Subtilisin BPN 281 I Ubtilisin-chymotrypsin inhibitor-2A 63 2SIC 1.8 E Subtilisin BPN 275 I Streptomyces subtilisin inhibitor 107 1SPB 2.0 S Subtilisin BPN 264 P Subtilisin BPN prosegment 71 1R0R 1.1 E Subtilisin carlsberg 274 I Ovomucoid 51 1CSE 1.2 E Subtilisin carlsberg 274 I Eglin-C 63 1SCJ 2.0 A Subtilisin E 275 B Subtilisin E 71 2SNI 2.1 E Subtilisin novo 275 I Chymotrypsin inhibitor 2 64 1EUC 2.1 B Succinyl-coa synthetase beta chain 393 A Succinyl-coa synthetase alpha chain 306 1ONQ 2.2 A T-cell surface glycoprotein CD1A 274 B Beta-2-microglobulin 99 1JTD 2.3 A Tem-1 beta-lactamase 262 B Beta-lactamase inhibitor protein II 273 1KTZ 2.2 B TGF-beta type II receptor 106 A Transforming growth factor beta 3 82 2TEC 2.0 E Thermitase 279 I Eglin-C 63 1JKG 1.9 B Tip associating protein 180 A NTF2-related export protein 1 139 1D4V 2.2 B TNF-related apoptosis inducing ligand 163 A Death receptor 5 117 1AVW 1.8 A Trypsin 223 B Trypsin inhibitor 171 1BRB 2.1 E Trypsin 223 I BPTI 51 1F5R 1.7 A Trypsin II 216 I Pancreatic trypsin inhibitor 57 1K9O 2.3 E Trypsin II anionic 223 I Alaserpin 376 1D6R 2.3 A Trypsinogen 223 I Bowman-birk proteinase inhibitor 58 1OPH 2.3 B Trypsinogen 223 A Alpha-1 protease inhibitor 375 1P2J 1.4 A Trypsinogen 220 I Pancreatic trypsin inhibitor 56 1S1Q 2.0 A Tumor susceptibility gene 101 protein 137 B Ubiquitin 71 1ITB 2.5 B Type 1 interleukin-1 receptor 310 A Interleukin-1 beta 153 1J7D 1.9 B Ubiquitin-conjugating enzyme E2-17 KDA 149 A MMS2 140 1EUV 1.3 A ULP1 protease 221 B Ubitqutin-like protein SMT3 79 1UGH 1.9 E Uracil-dna glycosylase 223 I Uracil-DNA glycosylase inhibitor 82 1UZX 1.9 A Vacuolar protein sorting-associated protein 135 B Ubiquitin 75 1JTT 2.1 A VH single-domain antibody 133 L Lysozyme 129 1RKE 2.4 A Vinculin 262 B VCL protein 176 1MA9 2.4 A Vitamin D-binding protein 442 B Actin alpha skeletal muscle 356 1YVN 2.1 A Yeast actin 372 G Gelsolin 125 1OXB 2.3 A YDP1P 166 B Osmolarity two-component system protein 124 Homodimers PDB code Resolution(Å) Name of Homodimer Scientific source Chain one Length Chain two Length 1CNZ 1.8 3-isopropylmalate dehydrogenase Salmonella typhimurium A 363 B 363 1AFW 1.8 3-ketoacetyl-coa thiolase Saccharomyces cerevisiae A 390 B 393 1M4I 1.5 Acetyltransferase Escherichia coli A 181 B 176 1LQ9 1.3 Actva-orf6 monooxygenase Streptomyces coelicolor A 112 B 112 1ADE 2 Adenylosucinate synthetase Escherichia coli A 431 B 431 1M7H 2 Adenylylsulfate kinase Penicillium chrysogenum A 203 B 200 1NA8 2.3 ADP-ribosylation binding protein Homo sapiens A 151 B 145 1OR4 2.2 Aerotactic transducer hemat Bacillus subtilis A 169 B 158 1BD0 1.6 Alanine racemase Bacillus stearothermophilus A 381 B 380 1A4U 1.9 Alcohol dehydrogenase Drosophila lebanonensis A 254 B 254 1ALK 2 Alkaline phosphatase Escherichia coli A 449 B 449 1LK9 1.5 Alliin lyase Allium sativum A 425 B 427 1HSS 2.1 Alpha-amylase inhibitor Triticum aestivum A 111 B 111 1S2Q 2.1 Amine oxidase B Homo sapiens A 499 B 494 1EKP 2.5 Amino acid aminotransferase Homo sapiens A 365 B 365 2GSA 2.4 Aminotransferase Synechococcus SP A 427 B 427 1DQT 2 Antigen Mus musculus A 117 B 117 1BJW 1.8 Aspartate aminotransferase Thermus thermophilus A 381 B 381 1JFL 1.9 Aspartate racemase Escherichia coli A 228 B 228 1MJH 1.7 Atp-binding protein Methanococcus jannaschii A 143 B 144 1IRI 2.4 Autocrine motility factor Homo sapiens A 557 B 557 1LR5 1.9 Auxin binding protein Zea mays A 160 B 160 1N80 2.5 Baseplate structural protein Bacteriophage T4 A 328 B 328 1EWZ 2.4 Beta lactamase oxa-10 Pseudomonas aeruginosa A 243 C 243 1EBL 1.8 Beta-ketoacyl-acp Synthase III Escherichia coli A 309 B 309 1N1B 2 Bornyl diphosphate synthase Salvia officinalis A 516 B 519 1KSO 1.7 Calcium-binding protein A3 Homo sapiens A 93 B 93 1JD0 1.5 Carbonic anhydrase Homo sapiens A 260 B 259 1AUO 1.8 Carboxylesterase Pseudomonas fluorescens A 218 B 218 1CDC 2 CD2 Rattus norvegicus A 96 B 96 1F13 2.1 Cellular coagulation factor Homo sapiens A 722 B 719 1NW1 2 Choline kinase Caenorhabditis elegans A 365 B 357 1R5P 2.2 Circadian oscillation regulator Anabaena SP A 90 B 93 1G64 2.1 Cob(I) alamin adenosyltransferase Salmonella typhimurium A 169 B 190 1OTV 2.1 Coenzyme pqq synthesis protein C Klebsiella pneumoniae A 254 B 254 1I0R 1.5 Conserved hypothetical protein Archaeoglobus fulgidus A 161 B 168 1OAC 2 Copper amine oxidase Escherichia coli A 719 B 722 1EAJ 1.4 Coxsackie virus Homo sapiens A 124 B 120 1CHM 1.9 Creatinase Pseudomonas putida A 401 B 401 1S44 1.6 Crustacyanin A1 subunit Homarus gammarus A 180 B 180 1GD7 2 CSAA protein Thermus thermophilus A 109 B 109 1L5B 2 Cyanovirin-N Nostoc ellipsosporum A 101 B 101 1SO2 2.4 Cyclic Phosphodiesterase B Homo sapiens A 363 B 363 1P3W 2.1 Cysteine desulfurase Escherichia coli A 385 B 385 1COZ 2 Cytidylyltransferase Bacillus subtilis A 126 B 126 1P6O 1.1 Cytosine deaminase Saccharomyces cerevisiae A 156 B 161 2DAB 2 D-amino acid aminotransferase Thermophilic bacillus A 280 B 282 1F17 2.3 Dehydrogenase Homo sapiens A 293 B 291 2NAC 1.8 Dehydrogenase Methylotrophic bacterium pseudomonas A 374 B 374 1NFZ 2 Delta-isomerase Escherichia coli A 176 B 180 1D1G 2.1 Dihydrofolate reductase Thermotoga maritima A 164 B 164 1DOR 2 Dihydroorotate dehydrogenase A Lactococcus lactis A 311 B 311 1AD1 2.2 Dihydropteroate synthetase Staphylococcus aureus A 264 B 251 1NU6 2.1 Dipeptidyl peptidase Homo sapiens A 728 B 728 1PE0 1.7 DJ-1 Homo sapiens A 187 B 187 1G1A 2.5 DTDP-D-glucose 4,6-Dehydratase Salmonella enterica A 352 B 352 1BBH 1.8 Electron transport Chromatium vinosum A 131 B 131 1Q8R 1.9 Endodeoxyribonuclease rusa Escherichia coli A 118 B 109 1RVE 2.5 Endonuclease Escherichia coli A 244 B 244 1M9K 2 Endothelial nitric-oxide synthase Homo sapiens A 400 B 401 1P43 1.8 Enolase 1 Saccharomyces cerevisiae A 436 B 436 1JR8 1.5 Erv2 protein mitochondrial Saccharomyces cerevisiae A 105 B 105 1V26 2.5 Fatty-acid-coa synthetase Thermus thermophilus A 489 B 510 1LBQ 2.4 Ferrochelatase Saccharomyces cerevisiae A 356 B 354 1RYA 1.3 Gdp-mannose mannosyl hydrolase Escherichia coli A 160 B 160 1QFH 2.2 Gelation factor Dictyostelium discoideum A 212 B 212 1JV3 2.2 Glcnac1p uridyltransferase Homo sapiens A 490 B 484 1DPG 2 Glucose 6-phosphate dehydrogenase Leuconostoc mesenteroides A 485 B 485 1QXR 1.7 Glucose-6-phosphate isomerase Pyrococcus furiosus A 187 B 187 1EOG 2.1 Glutathione S-transferase Escherichia coli A 208 B 208 1N2A 1.9 Glutathione S-transferase Escherichia coli A 201 B 187 1M0W 1.8 Glutathione synthetase Saccharomyces cerevisiae A 481 B 479 1R9C 1.8 Glutathione transferase Mesorhizobium loti A 125 B 118 1F4Q 1.9 Grancalcin Homo sapiens A 161 B 165 1DQP 1.8 Guanine phosphoribosyltransferase Giardia lamblia A 230 B 230 3SDH 1.4 Hemoglobin Scapharca inaequivalvis A 145 B 145 1IPI 2.2 Holliday junction resolvase Pyrococcus furiosus A 114 B 114 1FWL 2.3 Homoserine kinase Methanococcus jannaschii A 296 B 296 2HHM 2.1 Hydrolase Homo sapiens A 272 B 272 1PP2 2.5 Hydrolase Crotalus atrox R 122 L 122 1FJH 1.7 Hydroxysteroid dehydrogenase Comamonas testosteroni A 236 B 236 1G0S 1.9 Hypothetical Protein Escherichia coli A 201 B 202 1JOG 2.4 Hypothetical protein Haemophilus influenzae A 129 B 129 1PT5 2 Hypothetical protein Escherichia coli A 415 B 415 1QYA 2 Hypothetical Protein Escherichia coli A 293 B 307 1FUX 1.8 Hypothetical protein Escherichia coli A 164 B 163 1J30 1.7 Hypothetical rubrerythrin Sulfolobus tokodaii A 141 B 137 1LHZ 2.3 Immunoglobulin lambda Homo sapiens A 213 B 213 1AA7 2.1 Influenza virus matrix mrotein Influenza virus A 158 B 157 8PRK 1.9 Inorganic pyrophosphatase Saccharomyces cerevisiae A 282 B 282 1R8J 2 Kaia Synechococcus elongatus A 272 B 264 1CQS 1.9 Ketosteroid isomerase Pseudomonas putida A 124 B 124 1AQ6 2 L-2-haloacid dehalogenase Xanthobacter autotrophicus A 245 B 245 1I2W 1.7 Lactamase Bacillus licheniformis A 255 B 256 1BH5 2.2 Lactoylglutathione lyase Homo sapiens A 177 B 182 1QMJ 2.2 Lectin Gallus gallus A 132 B 132 1K75 1.8 L-histidinol dehydrogenase Escherichia coli A 425 B 425 1EHI 2.4 Ligase Leuconostoc mesenteroides A 360 B 347 1NWW 1.2 Limonene-1,2-epoxide hydrolase Rhodococcus erythropolis A 145 B 146 1UC8 2 Lysine biosynthesis enzyme Thermus thermophilus A 240 B 239 1EN5 2.3 Manganese superoxide dismutase Escherichia coli A 205 B 205 1A4I 1.5 Methylenetetrahydrofolate Homo sapiens A 285 B 295 1FC5 2.2 Molybdopterin biosynthesis Escherichia coli A 397 B 396 1JYS 1.9 Mta/sah nucleosidase Escherichia coli A 226 B 226 1LNW 2.1 Multidrug resistance operon repressor Pseudomonas aeruginosa A 137 B 135 1FP3 2 N-acyl-d-glucosamine Sus scrofa A 402 B 402 1FYD 2.3 NAD(+) Synthetase Bacillus subtilis A 271 B 246 1HJ3 1.6 Nitrite reductase Paracoccus pantotrophus A 544 B 542 1G1M 2.3 Nitrogenase iron protein Azotobacter vinelandii A 287 B 289 1G8T 1.1 Nuclease SM2 isoform Seratia marcencsens A 241 B 241 1EYV 1.6 N-utilizing substance protein Mycobacterium tuberculosis A 131 B 133 1M98 2.1 Orange carotenoid protein Arthrospira maxima A 316 B 314 1ORO 2.4 Orotate phosphoribosyltransferase Escherichia coli A 213 B 206 1DVJ 1.5 Orotidine 5'-phosphate decarboxylase Methanobacterium thermoautotrophicum A 239 B 211 1GGQ 2.5 Outer surface protein C Borrelia burgdorferi A 162 B 162 1AOR 2.3 Oxidoreductase Pyrococcus furiosis A 605 B 605 1BMD 1.9 Oxidoreductase Thermus flavus A 327 B 327 1HDY 2.5 Oxidoreductase Homo sapiens A 374 B 374 1N2O 2.1 Pantothenate synthetase Mycobacterium tuberculosis A 279 B 279 1RN5 2.2 Peptide deformylase Leptospira interrogans A 177 B 177 1PN2 2 Peroxisomal hydratase Candida tropicalis A 269 B 267 1PN0 1.7 Phenol 2-monooxygenase Trichosporon cutaneum A 652 C 656 1BXG 2.3 Phenylalanine dehydrogenase Rhodococcus SP A 349 B 347 1M6P 1.8 Phosphate receptor Bos Taurus A 146 B 146 1RQL 2.4 Phosphonoacetaldehyde hydrolase Bacillus cereus A 257 B 257 1O4U 2.5 Phosphoribosyltransferase Thermotoga maritima A 265 B 266 1EZ2 1.9 Phosphotriesterase Pseudomonas diminuta A 328 B 328 1EXQ 1.6 Pol polyprotein Escherichia coli A 147 B 145 1MNA 1.8 Polyketide synthase Streptomyces venezuelae A 276 B 278 1C6X 2.5 Protease Escherichia coli A 99 B 99 1FL1 2.2 Protease Escherichia coli A 192 B 207 1F89 2.4 Protein YLC351C Saccharomyces cerevisiae A 271 B 271 1LHP 2.1 Pyridoxal kinase Ovis aries A 306 B 309 1CBK 2 Pyrophosphokinase Haemophilus influenzae A 160 B 160 1QR2 2.1 Quinone reductase type 2 Homo sapiens A 230 B 230 1EN7 2.4 Recombination endonuclease Bacteriophage T4 A 157 B 157 1EV7 2.4 Restriction endonuclease naei Nocardia aerocolonigenes A 295 B 293 1H8X 2 Ribonuclease Homo sapiens A 125 B 125 1I4S 2.2 Ribonuclease III Aquifex aeolicus A 147 B 147 1KGN 1.9 Ribonucleotide reductase protein Corynebacterium ammoniagenes A 296 B 296 1TLU 1.6 S-adenosylmethionine decarboxylase Thermotoga maritima A 117 B 117 1K6Z 2 Secretion chaperone syce Yersinia pestis A 120 B 119 1K3S 1.9 Sige Salmonella enterica A 106 B 104 1PJQ 2.2 Siroheme synthase Salmonella typhimurium A 447 B 454 1HJR 2.5 Site-specific recombinase Escherichia coli A 158 C 158 3LYN 1.7 Sperm lysine Haliotis fulgens A 122 B 124 2SQC 2 Squalene-hopene Cyclase Alicyclobacillus acidocaldarius A 623 B 623 1SCF 2.2 Stem cell factor Homo sapiens A 116 B 118 1OX8 2.2 Stringent starvation protein B Escherichia coli A 105 B 105 1M3E 2.5 Succinyl-coa Sus scrofa A 459 B 460 1R7A 1.8 Sucrose phosphorylase Bifidobacterium adolescentis A 503 B 503 1SOX 1.9 Sulfite oxidase Gallus gallus A 463 B 458 1L5X 2 Survival protein E Pyrobaculum aerophilum A 270 B 272 1REG 1.9 T4 rega Bacteriophage T4 X 122 Y 120 1MKB 2 Thiol ester dehydrase Escherichia coli A 171 B 171 1QHI 1.9 Thymidine kinase Herpes simplex virus A 304 B 308 1HSJ 2.3 Transcription/sugar binding protein Escherichia coli A 487 B 487 1NY5 2.4 Transcriptional regulator Aquifex aeolicus A 384 B 385 1ON2 1.6 Transcriptional regulator Bacillus subtilis A 135 B 135 1SMT 2.2 Transcriptional repressor Synechococcus A 98 B 101 1TRK 2 Transferase Saccharomyces cerevisiae A 678 B 678 7AAT 1.9 Transferase Gallus gallus A 401 B 401 1KIY 2.4 Trichodiene synthase Fusarium sporotrichioides A 354 B 354 1I8T 2.4 Udp-galactopyranose mutase Escherichia coli A 367 B 367 1F6D 2.5 Udp-n-acetylglucosamine Escherichia coli A 366 B 363 1JP3 1.8 Undecaprenyl pyrophosphate synthase Escherichia coli A 210 B 207 1JMV 1.9 Universal stress protein A Haemophilus influenzae A 140 B 137 1HQO 2.3 URE2 protein Saccharomyces cerevisiae A 221 B 217 9WGA 1.8 Wheat germ agglutinin Triticum vulgaris A 170 B 170 1MI3 1.8 Xylose reductase Candida tenuis A 319 B 319 Figure 1 Difference between heterodimer and homodimer interface properties is shown.

Publication Year: 2005


Alignment of non-covalent interactions at protein-protein interfaces.

(2008) PLoS One 3

PubMed: 18382693 | PubMedCentral: PMC2274958 | DOI: 10.1371/journal.pone.0001926

A) Superposed inhibitors and catalytic triads for chymotrypsin (1acb) and subtilisin (1lw6) according to the Galinter alignment.

We have analyzed the interactions formed between chymotrypsin and leech proteinase inhibitor eglin c (PDB code: 1acb, chains E and I), and subtilisin with chymotrypsin inhibitor 2 (PDB code: 1lw6, chains E and I).

Publication Year: 2008


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


Computational study for protein-protein docking using global optimization and empirical potentials.

(2008) Int J Mol Sci 9

PubMed: 19325720 | PubMedCentral: PMC2635596 | DOI: null

of acceptable 1A0O 4.10 0 4.16 0 3.08 1 1ACB 1.33 D 6 0.97 9 1.28 8 1AVZ 5.73 0 4.79 0 4.90 0 1BRC 5.29 0 4.04 0 5.03 0 1BRS 10.47 0 4.96 0 7.67 0 1CGI 3.46 3 2.73 5 2.94 1 1CHO 4.02 0 1.11 3 1.45 2 1... SE 3.29 2 1.27 2 1.62 3 1MEL 9.38 0 3.66 1 7.31 0 1PPE 4.07 0 3.11 6 2.40 8 1STF 4.98 0 4.95 0 4.96 0 1TAB 5.86 0 4.98 0 5.97 0 1TGS 1.64 1 5.87 0 5.24 0 1UDI 2.14 4 4.05 0 2.25 4 2KAI 5.66 0 5.28 0 5.55 0 2PTC 5.29 0 4.98 0 5.61 0 2TEC 2.63 4 2.60 1 2.37 3 4HTC 6.14 0 7.54 0 3.57 1 A complex pdb stands for the pdb ID of the native structure of the corresponding complex-complex structures B The RMSD is defined as the RMSD over C α atoms of the interface residues between a predicted structure and its native complex and the smallest RMSD is the RMSD value calculated for the most native-like conformation in the final set C The number of the acceptable native-like structures found in the final set of 500 conformations D The smallest RMSD being “acceptable” is written with bold italic types.

Publication Year: 2008


A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.

(2007) Proteins 69

PubMed: 17623864 | PubMedCentral: PMC2673351 | DOI: 10.1002/prot.21498

Table I The Number of Top 5 Decoys with rmsd < 10 Å given by EMPIRE and the RosettaDock scoring function Pdb ID a 1CGI 1CHO 2PTC 1TGS 2SNI 2SIC 1CSE 2KAI EMPIRE b 1 5 4 5 5 5 5 5 Roset... aDock c 4 3 2 5 4 5 2 4 Pdb ID 1BRC 1ACB 1BRS 1MAH 1UGH 1DFJ 1FSS 1AVW EMPIRE 5 3 4 5 5 5 3 5 RosettaDock 1 2 4 5 5 4 5 5 Pdb ID 1PPE 1TAB 1UDI 1STF 2TEC 4 HTC 1MLC 1WEJ EMPIRE 5 5 5 5 5 5 2 2 RosettaDock 5 5 5 5 5 5 0 0 Pdb ID 1AHW 1DQJ 1BVK 1FBI 2JEL 1BQL 1JHL 1NQA EMPIRE 0 1 1 5 5 2 1 5 RosettaDock 5 2 5 3 5 5 1 5 Pdb ID 1NMB 1MEL 2VIR 1EO8 1QFU 1IAI 2PCC 1WQ1 EMPIRE 5 5 3 1 4 3 4 4 RosettaDock 5 5 4 1 5 0 3 3 Pdb ID AVZ 1MDA 1IGC 1ATN 1GLA 1SPB 2BTF 1A0Q EMPIRE 0 4 1 5 5 5 3 4 RosettaDock 0 3 2 5 1 5 4 1 Pdb ID 1BTH 1FIN 1FQ1 1GOT 1EFU 3HHR #(≥3) d #(>) EMPIRE 0 0 4 5 2 2 39 21 e RosettaDock 0 0 2 0 0 0 34 10 f a Enzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR).

Publication Year: 2007


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

(2009) BMC Bioinformatics 10

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

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 ... - - - 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 .

PDB a) Class b) Difficulty c) #Atoms (R, L) d) ΔASA (Å 2 ) e) 3DZD Correlation for Bound interface 3DZD Correlation for Unbound interface 1AY7 ( 1RGH ; 1A19 ) E E 747,721 1237 0.93 0.93 1CGI ( 2CGA ; 1HPT ) E E 1800,441 2053 0.96 0.97 2PCC ( 1CCP ; 1YCC ) E E 2339,847 1141 0.99 0.98 2SNI ( 1UBN ; 2CI2 ) E E 1932,521 1628 0.97 0.95 1ACB ( 2CGA ; 1EGL ) E MD 1799,575 1544 0.94 0.95 1AHW ( 1FGN ; 1TFH ) A E 3304,1622 1899 0.99 0.98 1FSK ( 1FSK ; 1BV1 ) A E 3347,1231 1623 0.95 0.89 1MLC ( 1MLB ; 3LZT ) A E 3290,1000 1392 0.97 0.96 1NCA ( 1NCA ; 7NN9 ) A E 3329,3067 1953 0.99 0.99 2JEL ( 2JEL ; 1POH ) A E 3297,640 1501 0.92 0.90 1KXP ( 1IJJ ; 1KW2 ) O E 2782,3527 3341 0.96 0.97 1IB1 ( 1QJB ; 1KUY ) O MD 3673,1312 2808 0.95 0.87 1WQ1 ( 6Q21 ; 1WER ) O MD 2534,1351 2913 0.92 0.93 1ATN ( 1IJJ ; 3DNI ) O D 2942,2036 1774 0.95 0.97 1DE4 ( 1A6Z ; 1CX8 ) O D 3064,1351 2066 0.98 0.97 a) The PDB IDs for the unbound proteins are shown in brackets.

Publication Year: 2009


Active site prediction using evolutionary and structural information.

(2010) Bioinformatics 26

PubMed: 20080507 | PubMedCentral: PMC2828116 | DOI: 10.1093/bioinformatics/btq008

To predict catalytic residues for the α-chymotrypsin structure 1acb, we estimated D iscern parameters using a subset of the CATRES-FAM dataset, removing all enzymes in the same SCOP superfamil... as 1acb.

In addition to these large-scale experiments, we present in the next section a detailed case study of Bovine α-Chymotrypsin (PDB id:1acb).

3.1 Bovine α-Chymotrypsin (PDB id:1acb, E.C. number: 3.4.121.1) Chymotrypsin (E.C. number 3.4.121.1) is the paradigmatic member of the so-called serine protease family of enzymes that are distinguished by having a catalytic triad of residues at the active site (H57, D102 and S195) (Hedstrom, 2002 ; Kraut, 1977 ; Polgar, 2005 ).

D iscern predictions on Bovine α-Chymotrypsin (PDB id:1acb).

Publication Year: 2010


Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.

(2010) BMC Bioinformatics 11

PubMed: 20459833 | PubMedCentral: PMC2885373 | DOI: 10.1186/1471-2105-11-242

The input motif consisted of the C α coordinates of the triad residues and was geometrically based upon the [PDB: 1ACB ] chymotrypsin structure; this motif was able to accurately identify tria... residues in all serine protease families, including cases where the triad residues span peptide chains.

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 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


Discriminative structural approaches for enzyme active-site prediction.

(2011) BMC Bioinformatics 12 Suppl 1

PubMed: 21342581 | PubMedCentral: PMC3044306 | DOI: 10.1186/1471-2105-12-S1-S49

Residues Template log( F pints ) Deviation 1 HIS 57 A, ASP 102 A, GLY 193 A, SER 195 A 1acb –53.37 0.83 2 ASP 137 A, ASP 194 A 1qk2 –14.00 0.66 3 ASP 137 A, ASP 194 A 2bvw –12.... 6 0.69 4 ASP 100 A, ASP 97 A 1qk2 –7.77 0.85 5 ASP 189 A, HIS 172 A 1emh –6.60 1.10 6 ASP 102 A, ASP 97 A 1qk2 –5.18 0.95 7 ASP 239 A, ASP 128 A 1qk2 –5.11 0.95 8 ASP 194 A, ASP 189 A 2bvw –5.08 0.96 9 ASP 97 A, HIS 57 A 1emh –2.79 1.25 10 ASP 61 A, HIS 40 A 1emh –2.62 1.26 Protein structure 1bio is used to generate this example.

Publication Year: 2011


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 Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Predicting protein interactions by Brownian dynamics simulations.

(2012) J Biomed Biotechnol 2012

PubMed: 22500075 | PubMedCentral: PMC3303761 | DOI: 10.1155/2012/121034

Complex PDB Res (Å) Receptorname Ligandname Docking results Crystal structures RMSD a (Å) Interaction energy (kcal mol −1 ) RMSD (Å) Interaction energy (kcal mol "... 2;1 ) Sequence number/total number b Protease-inhibitor  1CA0 2.10 Chymotrypsin APPI 1.27 −93.70 0.84 −93.22 116522/492124  1CBW 2.60 Chymotrypsin BPTI 0.54 −83.51 0.19 −85.02 171485/456398  1ACB 2.00 Chymotrypsin Eglin C 1.00 −103.41 0.70 −103.49 382613/513612  1CHO 1.80 Chymotrypsin Ovonmuciod 0.30 −102.35 0.38 −102.42 302176/406978  1CGI 2.30 Chymotrypsinogen HPTI 0.18 −147.17 0.15 −147.10 34660/494274  2KAI 2.50 Kallikrein A BPTI 1.10 −114.68 0.21 −113.85 422991/576133  2SNI 2.10 Subtilisin BPN CI-2 0.27 −108.81 0.28 −108.86 232574/428140  2SIC 1.80 Subtilisin BPN SSI 0.89 −94.41 0.20 −104.20 109196/440000  1CSE 1.20 Subtilisin Carlsberg Eglin C 1.24 −98.28 0.088 −103.19 284340/470409  2TEC 1.98 Thermitase Eglin C 0.44 −108.55 0.68 −109.99 341844/565586  1TAW 1.80 Trypsin (bovine) APPI 1.10 −97.13 0.86 −97.14 374416/448887  2PTC 1.90 Trypsin (bovine) BPTI 0.98 −96.22 0.36 −96.25 269684/377757  3TGI 1.80 Trypsin (rat) BPTI 0.39 −102.43 0.52 −102.44 232589/511269  1BRC 2.50 Trypsin (rat) APPI 1.43 −90.55 0.55 −90.04 120053/527160 Enzyme-inhibitor  1FSS 3.00 Acetylcholinesterase Fasciculin II 0.17 −137.88 0.20 −137.88 356416/364018  1BVN 2.50 α -Amylase Tendamistat 0.25 −142.67 0.24 −142.51 202279/297696  1BGS 2.60 Barnase Barstar 0.48 −112.46 0.57 −112.37 326865/408756  1AY7 1.70 Ribonuclease sa Barstar 0.49 −77.41 0.51 −77.37 9999/356359  2B5R 1.70 TEM-1 lactamase BLIP 0.78 −154.04 0.37 −158.39 369/464219  1UGH 1.90 UDG UGI 0.54 −135.58 0.51 −135.43 120973/427026 Electron transport  2PCB c 2.80 Cyt c Peroxidase Cytochrome c 1.98 −87.18 0.22 −81.79 6060/416861  2PCF NMR Cytochrome f Plastocyanin 0.28 −118.96 0.23 −119.32 83197/208700 Antibody-antigen  1MLC 2.10 Fab D44.1 Lysozyme 1.59 −93.99 0.44 −95.80 75843/344243  1VFB d 1.80 Fv D1.3 Lysozyme 0.53 −84.78 0.43 −84.59 517225/1195007 a RMSDs are calculated for the C α atoms of the ligand protein since the receptor proteins are always fixed during the simulations.

Complex PDB RMSD (Å) a Other docking methods ICM b Nussinov c FTDOCK d BiGER e Protease-inhibitor  1CA0 0.44 0.4 — — —  1CBW 0.24 0.5 — —  1ACB 0.58 0.5 0.9 — 0.6  1CHO 0.26 0.3 0.5 0.8 —  1CGI 0.15 0.4 — 1.0 —  2KAI 0.30 0.8 1.2 0.4  2SNI 0.16 0.3 1.1 0.6 —  2SIC 0.58 0.4 1.1 0.8 3.8  1CSE 0.53 0.3 1.3 — —  2TEC 0.18 0.3 1.2 — 3.6  1TAW 0.39 0.7 — — —  2PTC 0.72 0.4 0.6 0.7  3TGI 0.21 0.3 — — —  1BRC 0.55 0.7 — — — Enzyme-inhibitor  1FSS 0.13 0.4 — — —  1BVN 0.23 0.4 — — —  1BGS 0.33 0.6 — —  1AY7 0.30 0.7 — —  2B5R 0.60 1.3 — — —  1UGH 0.39 0.4 — — — Electron transport  2PCB 1.18 1.2 — — —  2PCF 0.19 1.1 — — — Antibody-antigen  1MLC 0.57 0.4 — 0.8 —  1VFB 0.24 0.5 1.5 0.7 — a RMSDs are calculated for the ligand interface C α atoms in this work.

Complex PDB Crystal packing Without packing RMSD*(Å) Interaction energy (kcal mol −1 ) RMSD*(Å) Interaction energy (kcal mol −1 ) 1CBW 0.72 −161.60 0.54 −83.51 1ACB 0.49 −131.61 1.00 −103.41 1CHO 0.23 −140.39 0.30 −102.35 1CGI 1.07 −138.82 0.18 −147.17 2KAI 0.98 −140.16 1.10 −114.68 2SNI 0.58 −120.52 0.27 −108.81 2SIC 1.44 −103.29 0.89 −94.41 2TEC 0.76 −127.74 0.44 −108.55 1TAW 0.44 −103.90 1.10 −97.13 1FSS 0.26 −175.90 0.17 −137.88 *RMSDs are calculated for the C α atoms of the ligand protein.

Publication Year: 2012


DelPhi: a comprehensive suite for DelPhi software and associated resources.

(2012) BMC Biophys 5

PubMed: 22583952 | PubMedCentral: PMC3463482 | DOI: 10.1186/2046-1682-5-9

In order to determine the minimal requirement of computational time cost for DelPhi to achieve results within a desired accuracy, a series of tests were designed and implemented on a typical protein o... medium size, namely the bovine alpha-chymotrypsin-eglin C complex [PDB:1ACB], to demonstrate the performance of DelPhi.

Publication Year: 2012


Protein-protein binding site identification by enumerating the configurations.

(2012) BMC Bioinformatics 13

PubMed: 22768846 | PubMedCentral: PMC3478195 | DOI: 10.1186/1471-2105-13-158

h The binding sites between chain E and chain I of 1acb are predicted by each method; Two unbound structures are chain B of 2cga and the only one chain of 1egl.

Publication Year: 2012


Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.

(2012) BMC Bioinformatics 13

PubMed: 22984947 | PubMedCentral: PMC3479416 | DOI: 10.1186/1471-2105-13-236

The bound structure of the alpha-chymotrypsin is 1acb [ 34 ], and the unbound structure is 1gct [ 35 ].

Publication Year: 2012


Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.

(2012) BMC Struct Biol 12

PubMed: 23217202 | PubMedCentral: PMC3532097 | DOI: 10.1186/1472-6807-12-31

The protein complex, the bovine α-chymotrypsin-eglin C, PDB ID 1ACB, was placed onto these objects, just touching the surface.

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


On the importance of polar interactions for complexes containing intrinsically disordered proteins.

(2013) PLoS Comput Biol 9

PubMed: 23990768 | PubMedCentral: PMC3749945 | DOI: 10.1371/journal.pcbi.1003192

(c) Ribbon structure of one of the 3D complexes, α-chymotrypsin (grey) and eglin c (gold) (bovine α-chymotrypsin; PDB: 1ACB chain E, Rg = 16 Å, N =... 0a;241).

Publication Year: 2013


MEGADOCK 3.0: a high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments.

(2013) Source Code Biol Med 8

PubMed: 24004986 | PubMedCentral: PMC3847482 | DOI: 10.1186/1751-0473-8-18

For measuring thread parallel scalability, we conducted dockings of a protein complex from PDB, 1ACB (chain E and I).

Publication Year: 2013


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).

Rigid-body (21) 1AK4, 1AVX, 1AY7, 1B6C, 1CGI, 1D6R, 1E96, 1EAW, 1EWY, 1GCQ, 1GHQ, 1HE1, 1KAC, 1KTZ, 1PPE, 1SBB, 1UDI, 2PCC, 2SIC, 2SNI, 7CEI Medium Difficulty (2) 1ACB, 1GRN Table 3 The 44 complex structures selected from the ZLAB Benchmark 2.0 dataset (small dataset).

Publication Year: 2014


Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.

(2004) BMC Bioinformatics 5

PubMed: 15606919 | PubMedCentral: PMC544855 | DOI: 10.1186/1471-2105-5-205

All are proteins from hydrolase-inhibitor complexes, with six being proteinases: 1acb_E [ 40 ] (chain E of PDB structure 1acb), 1fle_E[ 41 ], 1hia_A[ 42 ], 1avw_A[ 43 ], 2sic_E[ 44 ], 3sgb_E [ 18 ]; a... d one being a carboxypeptidase: 4cpa [ 45 ].

Publication Year: 2004