Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Variability in docking success rates due to dataset preparation.

(2012) J Comput Aided Mol Des 26

PubMed: 22566074 | PubMedCentral: PMC3397132 | DOI: 10.1007/s10822-012-9570-1

One example of a crucial bridging water in the ACS-Astex set is PDB code 1G9V (shown in Fig.

Table 1 Complexes requiring additional preparation Inconsistent stereo configuration  1GKC 1L7F 1R55 1VCJ  1GM8 1M2Z 1R58 1W1P  1GPK 1MMV 1R9O 1W2G  1HP0 1OF1 1S19 1X8X  1HVY 1OF6 1S3V 1XM6  1HWI 1OYT 1SQ5 1YGC  1HWW 1P2Y 1SQN 1YQY  1K3U 1P62 1TT1 1YV3  1KE5 1Q1G 1UML 1YWR  1KZK 1R1H 1V0P Co-factors with incorrect number of hydrogens  1G9V 1KZK 1Q1G 1W1P  1HWI 1M2Z 1Q4G 1W2G  1IA1 1MMV 1R9O 1XM6  1J3J 1OPK 1T9B 1XOQ  1JJE 1P62 1TZ8 Alternate locations missing hydrogens  1GM8 1OPK 1T9B 1XOZ  1HNN 1OQ5 1TZ8 1Y6B  1HP0 1Q4G 1UOU 1YV3  1IA1 1R1H 1VCJ 1YWR  1KZK 1S19 1W1P 1Z95  1L2S 1S3V 1X8X 2BR1  1N46 1T46 1XOQ The ‘modified’ ACS-Astex dataset Upon closer examination of some of the complexes it was noted that the hydrogen bond network was not optimal and therefore further optimization was warranted.

Table 6 Docking failures on corrected ACS-Astex set PDB code Failure type Minimum RMSD (Å) Present in binding site Top 1 Top 30 Water Metal 1g9v Placement 2.51 2.24 X 1gm8 Placement 3.20 2.69 X 1hp0 Scoring 2.93 1.07 X 1hvy Scoring 2.13 1.39 X 1jd0 Scoring 4.96 1.68 X 1l2s Scoring 3.65 0.80 1mzc Placement 3.66 2.92 X 1n2v Scoring 2.23 1.14 1oq5 Scoring 3.47 1.00 X 1owe Scoring 3.18 1.09 X 1q1 g Scoring 2.28 1.91 X 1r58 Placement 2.86 2.84 1sq5 Placement 4.96 2.55 X 1xm6 Scoring 2.40 0.50 X X 1y6b Placement 4.72 2.97 1ygc Placement 3.04 3.04 X Nearly half of the failure cases (8) were due to placement failure, where the docker was unable to generate any pose under 2 Å RMSD.

Publication Year: 2012


Automating crystallographic structure solution and refinement of protein-ligand complexes.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24419387 | PubMedCentral: PMC3919266 | DOI: 10.1107/S139900471302748X

In each case a single ligand species of interest is bound, although some structures also contain additional physiologically relevant ligands that are present in the starting models (such as haem in PD... entry 1g9v or an ATP analog in PDB entry 1hq2 ).

(ii) PDB entry 1g9v ran successfully, but the number of copies of ligands was manually specified because the estimated number of copies of the ligands was incorrect (owing to the use of the complete hemoglobin tetramer as the search model versus two ligands bound).

PDB code Re-refined R work / R free Pipeline R work / R free Placed/present Ligand r.m.s.d.(s) (Å) 1b9v 0.175/0.202 0.200/0.224 1/1 0.65 1br6 0.180/0.224 0.192/0.225 1/1 0.20 1cx2 0.245/0.308 0.250/0.362 0/4 — 1exa 0.169/0.192 0.182/0.213 1/1 0.06 1fcx 0.135/0.167 0.152/0.181 1/1 0.13 1fcz 0.141/0.175 0.157/0.182 1/1 0.08 1fjs 0.158/0.204 0.231/0.255 0/1 — 0.178/0.208 1/1 C 0.59 1g9v 0.141/0.166 0.135/0.171 1/2 0.17 0.136/0.171 2/2 C 0.16, 0.17 1hp0 0.163/0.216 0.173/0.227 2/2 P 0.31, 2.04 1hq2 0.121/0.160 0.134/0.166 1/1 0.10 1hwi 0.165/0.189 0.177/0.198 4/4 0.32–0.44 1hww 0.136/0.167 0.222/0.248 0/1 — 1k3u 0.135/0.162 0.137/0.165 1/1 0.05 1l2s 0.147/0.168 0.168/0.195 2/3 0.15, 0.16 1ml1 0.159/0.208 0.173/0.208 6/6 0.25–0.86 1mq6 0.171/0.221 0.184/0.227 1/1 P 1.36 0.179/0.230 1/1 C 0.68 1mzc 0.146/0.168 0.152/0.168 1/1 P 2.51 1n2j 0.168/0.193 0.185/0.210 2/2 0.10, 0.25 1of1 0.156/0.179 0.175/0.197 2/2 0.11, 0.13 1of6 0.173/0.191 0.208/0.230 8/8 0.11–1.82 1oq5 0.120/0.164 0.231/0.264 0/1 — 0.148/0.188 1/1 C 0.86 1pmn 0.190/0.224 0.218/0.249 1/1 0.53 1q1g 0.156/0.185 0.195/0.214 6/6 0.18–0.63 1q41 0.182/0.195 0.207/0.222 2/2 0.19, 0.30 1qhi 0.214/0.253 0.348/0.403 0/1 — 1r9o 0.162/0.193 0.240/0.284 1/1 0.39 1tt1 0.147/0.171 0.158/0.182 2/2 0.17, 0.19 1u4d 0.187/0.206 0.200/0.219 2/2 P 0.64, 0.67 1unl 0.190/0.214 0.264/0.291 0/1 — 0.246/0.276 1/1 C 0.98 1w1p 0.196/0.230 0.225/0.257 2/2 0.22, 0.30 1w2g 0.177/0.198 0.204/0.221 2/2 0.26, 0.56 1yqy 0.201/0.246 0.351/0.411 0/1 — 1yv3 0.151/0.184 0.169/0.193 1/1 0.19 2ack 0.159/0.185 0.446/0.507 — — 0.165/0.193 1/1 C 0.42 2br1 0.162/0.195 0.170/0.212 1/1 0.33 4cox 0.205/0.30 0.256/0.361 0/4 —

Publication Year: 2014