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Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble.

(2010) J Comput Aided Mol Des 24

PubMed: 20499135 | PubMedCentral: PMC2901495 | DOI: 10.1007/s10822-010-9365-1

For the goal of comparing different tools in their ability to reproduce the conformation of ligands in their bound states, conformers generated by OMEGA were subsequently clustered and the information... in the smaller number of cluster centers was compared to the information contained in the original OMEGA output Table 1 The protein data bank IDs from which the ligands were extracted, the number of rotatable bonds, the number of conformers Ligand Rotors omega a nmrclust b rms c rms_avg d Ligand Rotors omega a nmrclust b rms c rms_avg d 1CIM 1 8 4 4 4 1UVT 8 500 57 66 253 1QPE 2 2 2 2 1 1YDT 8 500 44 52 121 1YDR 2 25 7 11 12 2CGR 8 500 55 68 66 2PCP 2 5 5 5 3 3ERT 8 500 92 102 8 1F4E 3 26 6 6 5 1M48 9 500 48 48 54 1FCX 3 111 21 23 27 1NHU 9 500 47 54 104 1H1P 3 378 47 50 44 1NHV 9 500 88 99 113 1H9U 3 32 5 8 8 2QWI 9 500 35 35 15 1 JSV 3 68 16 18 24 1K1 J 10 500 57 64 142 1BR6 4 79 16 20 23 1KV2 10 500 72 72 44 1DLR 4 109 16 17 19 1MQ6 10 500 62 66 76 1FCZ 4 135 19 20 24 7DFR 10 500 78 84 28 1L2S 4 34 7 7 8 1EZQ 11 500 68 69 88 2CSN 4 88 10 10 11 1FKG 11 500 78 84 92 1K7E 5 75 19 23 10 1K22 11 500 54 60 33 1KV1 5 38 6 8 6 1QBU 11 500 66 69 118 1QL9 5 500 54 60 198 1HFC 12 500 54 59 50 1YDS 5 319 22 22 11 1MNC 12 500 55 55 57 5STD 5 331 48 54 29 1OHR 12 500 44 44 47 1EVE 6 500 37 46 31 1UVS 12 500 58 60 83 1F0T 6 500 64 68 262 7EST 12 500 62 68 29 1H1S 6 500 61 69 88 1ELA 13 500 39 45 25 1HDQ 6 45 9 12 6 1GWX 13 500 110 120 274 1K7F 6 500 75 80 52 1HPV 13 500 41 47 115 1A42 7 500 63 67 33 1O86 13 500 33 34 27 1IF7 7 500 70 82 179 1F4G 14 500 49 49 35 1L8G 7 500 36 36 50 1HTF 15 500 58 59 149 1LQD 7 500 60 65 182 1MMB 15 500 37 37 63 966C 7 500 52 56 45 Average 7.7 366.8 43.8 47.7 65.0 The number of conformers generally increased with the number of rotors for each method a Enumerated with recommended settings in OMEGA Generated by: b  Clustering the OMEGA conformers employing the NMRCLUST algorithm c Adjusting the rms parameter of OMEGA to generate similar numbers of conformers as the number of clusters identified by the NMRCLUST algorithm d Partitioning the dataset into low, medium and large numbers of rotatable bonds, averaging the rms values in each group and using the averaged rms values Next, the computational 3D models were built from scratch, and minimized employing the MMFF94x force field and default parameters in MOE.

Publication Year: 2010