BioLuminate

[…] with fixed ring conformation. ligand-receptor interaction energy was estimated by the mm-gbsa approach in prime module of schrödinger., the protein–protein docking was performed in the schrödinger bioluminate module (zhu et al., ) searching for the 30 best complexes within 70,000 (the default numbers) possible protein–protein configurations without constraints. the docking was performed […]

[…] the template []. the structural coordinates of the template were obtained from the protein data bank []. plyd1 mutations t65c, g293c and c428a were introduced into the wild-type 3d structure using bioluminate (release 2015–3, schrödinger, llc, new york, ny, 2015). for each substitution, all residues within a 4 å cut-off distance from the mutation site were refined in order to accommodate […]

[…] measures the net change in the binding free energy (δδgb) of a protein-protein complex upon mutation of amino acid residue to alanine. we have scanned all interface residue with schrodinger module bioluminate [], and two other web servers drugscoreppi [] and beatmusic []. we performed alanine scanning of all interface residues in both gata4 and nkx2.5 to find hotspot residues. we found […]

[…] described in ., molecular modeling was performed on a lenovo thinkpad t440p (lenovo) using schrödinger suite maestro (maestro, version 10.2, schrödinger, llc, 2015) and schrödinger biologics suite (bioluminate, version 1.9, schrödinger, llc, 2015). a human ddx3x model was generated based on the high-resolution structure pdb 2i4i (resolution, 2.2 å) using the protein preparation wizard (standard […]

[…] in the prep wiz module of maestro (version 9.1, schrodinger) and water molecules within 5 å of het groups were kept. subsequently, the residues of d12 and q61 were mutated into c12 and h61 using the bioluminate module of maestro, respectively. a grid file was generated based on the position of compound bzim in the grid generation wizard. then, 0375-0604 was prepared to assign atomic charges […]