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ACPYPE - AnteChamber PYthon Parser interfacE.

(2012) BMC Res Notes 5

PubMed: 22824207 | PubMedCentral: PMC3461484 | DOI: 10.1186/1756-0500-5-367

More importantly, this test shows that ACPYPE allows the structure determination of protein–ligand complexes with autogenerated parameters and topologies (for illustrative purposes, the struct... res for [PDB:1BVE] are shown in Figure 3 , the other structures are available in Additional file 4 ).

Table 1 Original NMR x ACPYPE             Comparison data [PDB:1BVE] [PDB:1IKU] [PDB:1JKN] [PDB:2JN3] [PDB:2K0G] PDB ligand code DMP MYR ATP JN3 CMP RMSD backbone (Å) 1.16/1.16 1.52/2.53 0.97/1.56 0.47/1.55 2.24/2.30 all atoms (Å) 1.88/2.04 2.23/ 3.33 1.60/2.38 1.39/2.40 2.53/2.79 Ramachandran core (%) 71.9/88.5 79.9/79.4 82.4/84.8 84.9/72.9 90.6/87.1 allowed (%) 24.7/9.8 17.6/16.4 16.9/12.7 13.6/22.3 8.9/12.1 generous (%) 2.9/1.1 2.1/2.5 0.5/1.9 1.4/2.9 0.5/0.3 disallowed (%) 0.5/0.6 0.4/ 1.6 0.2/0.7 0.0/2.2 0.0/0.5 NOE completeness (%) 41.3/45.9 51.7/55.8 53.6/55.4 44.9/45.3 49.6/50.4 CING ROG score green (%) 25/15 78/133 56/83 74/75 52/70 orange (%) 29/25 51/43 53/49 28/36 47/48 red (%) 46/60 60/13 57/34 25/16 44/25 Structure quality indicator changes for the original NMR structures from the PDB (left of /) to the structures recalculated using the ACPYPE parameters for the ligand (right of /).

Figure 3 Recalculated entry [PDB:1BVE] Entry [PDB:1BVE] from PDB recalculated using RECOORD protocol showing 25 models superimposed; picture created with VMD [ [ 45 ] ].

Publication Year: 2012