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PDB ID Mentions in PubMed Central Article count: 1

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

(2013) PLoS One 8

PubMed: 24204571 | PubMedCentral: PMC3804535 | DOI: 10.1371/journal.pone.0074830

PDB Loop N N contact a N out b N SC c N HB d Loop sequence Source PLOP/Rosetta benchmark 1a8d 155–166 12 4.8 2.9 1.9 1.4 DLPDKFNAYLAN [21] , [22] 1arb 182–193 12 5.2 4.2 1.3 2.1 WQPSGG... TEPGS [21] , [22] 1bhe 121–132 12 3.4 2.4 1.1 1.2 GQGGVKLQDKKV [21] , [22] 1bn8 298–309 12 3.8 2.5 0.9 0.8 STSSSSYPFSYA [21] , [22] 1c5e 82–93 12 2.9 2.4 1.1 0.9 YEDVLWPEAASD [21] , [22] 1cb0 33–44 12 3.8 2.8 1.4 1.4 YVDTPFGKPSDA [21] , [22] 1cnv 188–199 12 4.3 3.0 1.3 1.2 FYNDRSCQYSTG [21] , [22] 1cs6 145–156 12 2.8 2.7 1.4 1.1 NEFPNFIPADGR [21] , [22] 1dqz 209–220 12 3.1 2.6 0.8 0.8 CGNGTPSDLGGD [21] , [22] 1exm 291–302 12 4.1 2.6 1.4 1.3 RGVSREEVERGQ [21] , [22] 1f46 64–75 12 2.6 2.2 1.1 0.6 MVKPGTFDPEMK [21] , [22] 1i7p 63–74 12 3.9 3.1 1.1 1.2 LPSPQHILGLPI [21] , [22] 1m3s e 68–79 12 2.2 1.8 0.7 1.2 VGEILTPPLAEG [21] , [22] 1ms9 529–540 12 2.5 2.5 0.8 0.8 GSTPVTPTGSWE [21] , [22] 1my7 254–265 12 2.9 2.8 0.8 0.5 TPPYADPSLQAP [21] , [22] 1oth 69–80 12 2.7 2.3 0.8 1.0 QKGEYLPLLQGK [21] , [22] 1oyc 203–214 12 4.9 3.6 1.9 1.9 DPHSNTRTDEYG [21] , [22] 1qlw 31–42 12 2.9 1.4 0.8 1.0 ETLSLSPKYDAH [21] , [22] 1t1d 127–138 12 3.1 2.4 0.7 1.1 SGGRLRRPVNVP [21] , [22] 2pia 30–41 12 2.6 2.1 0.6 0.9 DPQGAPLPPFEA [21] , [22] Difficult cases 1alc 34–41 8 5.2 4.5 1.1 1.2 SGYDTQAI [21] , [58] 1msp 54–62 9 3.4 3.4 0.9 1.0 SVDPPCGVL [35] 1w7z 40952 12 1.9 1.9 0.8 0.6 CPRILIRCKQDS [33] , [59] f 2tgi 48–59 12 3.6 2.9 1.4 1.8 CPYLWSSDTQHS [22] , [60] 1ppn 175–186 12 4.9 3.1 1.9 1.2 NSWGTGWGENGY [36] , [61] f 1bni 75–86 12 4.2 2.7 1.4 1.6 DINYTSGFRNSD [62] , [63] f 2ci2 53–64 12 1.8 1.8 0.6 0.7 VGTIVTMEYRID [33] , [64] , [65] 1udg 152–163 12 3.8 2.1 1.2 1.5 VKRGAAASHSRI [66] f 1arp 290–307 18 3.1 2.8 1.1 0.8 LTDCSDVIPSAVSNNAAP [34] 1huw 47–64 18 2.4 1.9 1.1 1.0 NPQTSLCPSESIPTPSNK [60] 1rhd f 136–153 18 2.3 2.3 0.8 0.7 EGHPVTSEPSRPEPAIFK [60] 7cat 290–309 20 3.8 2.4 1.7 0.9 IFPFNPFDLTKVWPHGDYPL [60] 1thg 309–332 24 4.8 3.0 1.3 1.5 LFGLLPQFLGFGPRPDGNIIPDAA [22] , [60] 1c5e f 70–93 24 4.2 3.6 1.1 1.1 TTLTFYKSGTFRYEDVLWPEAASD [21] , [22] 1rhd 136–164 29 2.8 2.6 0.8 0.7 EGHPVTSEPSRPEPAIFKATLNRSLLKTY [60] Blind tests Test A 22–33 12 1.0 0.7 0.2 0.3 _g Blind g Test B 57–68 12 2.4 1.8 0.4 1.2 _g Blind g Test C 92–103 12 3.6 1.8 1.1 2.0 _g Blind g Test D 210–220 11 2.7 1.6 0.4 1.2 _g Blind g 3v7e 534–545 12 3.8 2.2 0.8 1.8 AKDADPILTSSV Blind [39] Mean 13.2 3.3 2.5 1.0 1.1 Median 12.0 3.1 2.5 1.1 1.1 For statistics N contact , N out , N SC , and N HB , residues with sequence positions within two residues of each loop residue were excluded from the calculation; only non-hydrogen atoms were considered.

Publication Year: 2013