PMC:4706832 / 5452-6309 JSONTXT

{"project":"2_test","denotations":[{"id":"28330089-10592235-401","span":{"begin":207,"end":211},"obj":"10592235"},{"id":"28330089-21812414-402","span":{"begin":324,"end":328},"obj":"21812414"},{"id":"28330089-16494871-403","span":{"begin":492,"end":496},"obj":"16494871"},{"id":"28330089-26620784-404","span":{"begin":832,"end":836},"obj":"26620784"},{"id":"28330089-16211538-405","span":{"begin":851,"end":855},"obj":"16211538"}],"text":"The three-dimensional (3D) structure of native and mutant (L1196M, G1269A) ALK structures were retrieved from the crystal structures of the Brookhaven Protein Data Bank (PDB) for the analysis (Berman et al. 2000). The corresponding PDB codes were 2XP2 and 4ANS for the native and mutant structures, respectively (Cui et al. 2011). Crizotinib was used as the small molecule for our study. The SMILES strings of the crizotinib and the lead molecules were collected from PubChem (Feldman et al. 2006) and submitted to CORINA for constructing the 3D structure of molecule (Gasteiger et al. 1990). The 3D structure of target proteins (2XP2 and 4ANS) drug molecule and lead compounds was energy-minimized using GROMACS package 4.5.3 adopting the GROMOS43a1 force field parameters before performing the computational analysis (Hess et al. 2008; Spoel et al. 2005)."}