Open SalahBioPhysics opened 7 years ago
@gregoryross @bas-rustenburg I want to put you in the loop of what we are looking at right now. Here (https://github.com/choderalab/PDBfinder/blob/master/kinase-pdbs/Imatinib-BCR-ABL/explicit_water_minimized/3PYY-minimized.pdb) you'll find the input PDB structure for Imatinib. We found the following vdw clashes:
STI+1B0001_001 807 | TYR01A0023_001 | -0.458 | 50.72 1649 | GLU01A0056_001 | -1.784 | 999.00 2338 | THR01A0085_001 | 1.667 | 68.10 3322 | ARG01A0132_001 | 0.145 | 45.09 3699 | ASP01A0151_001 | -0.431 | 64.55 | | | STI+2B0001_002 807 | TYR01A0023_001 | -0.427 | 50.72 1649 | GLU01A0056_001 | -1.61 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.75 2338 | THR01A0085_001 | 1.719 | 68.10 3322 | ARG01A0132_001 | 0.257 | 45.06 3699 | ASP01A0151_001 | -0.74 | 64.56 | | | | | | STI01B0001_003 807 | TYR01A0023_001 | -0.595 | 50.72 1649 | GLU01A0056_001 | -2.158 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.76 2338 | THR01A0085_001 | 2.28 | 68.10 3322 | ARG01A0132_001 | 0.045 | 45.10 3699 | ASP01A0151_001 | -0.563 | 64.58 | | | | | | STI+aB0001_004 807 | TYR01A0023_001 | -0.881 | 50.72 1649 | GLU01A0056_001 | -1.9 | 999.00 1728 | VAL01A0059_001 | 0 | 45.68 2338 | THR01A0085_001 | 1.607 | 68.09 3322 | ARG01A0132_001 | 0.157 | 45.09 3699 | ASP01A0151_001 | -0.234 | 64.55 | | | STI+bB0001_006 807 | TYR01A0023_001 | -0.847 | 50.72 1649 | GLU01A0056_001 | -1.762 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.75 2338 | THR01A0085_001 | 1.56 | 68.09 3322 | ARG01A0132_001 | 0.27 | 45.06 3699 | ASP01A0151_001 | -0.532 | 64.56
ASP01A0151_001: ASP res 3 letter code, A chain ID, 0151 res number, 001 conf number. We also have vdw clashes in other complexes.
@gregoryross @bas-rustenburg I want to put you in the loop of what we are looking at right now.
Here (https://github.com/choderalab/PDBfinder/blob/master/kinase-pdbs/Imatinib-BCR-ABL/explicit_water_minimized/3PYY-minimized.pdb) you'll find the input PDB structure for Imatinib. We found the following vdw clashes:
STI+1B0001_001 807 | TYR01A0023_001 | -0.458 | 50.72 1649 | GLU01A0056_001 | -1.784 | 999.00 2338 | THR01A0085_001 | 1.667 | 68.10 3322 | ARG01A0132_001 | 0.145 | 45.09 3699 | ASP01A0151_001 | -0.431 | 64.55 | | | STI+2B0001_002 807 | TYR01A0023_001 | -0.427 | 50.72 1649 | GLU01A0056_001 | -1.61 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.75 2338 | THR01A0085_001 | 1.719 | 68.10 3322 | ARG01A0132_001 | 0.257 | 45.06 3699 | ASP01A0151_001 | -0.74 | 64.56 | | | | | | STI01B0001_003 807 | TYR01A0023_001 | -0.595 | 50.72 1649 | GLU01A0056_001 | -2.158 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.76 2338 | THR01A0085_001 | 2.28 | 68.10 3322 | ARG01A0132_001 | 0.045 | 45.10 3699 | ASP01A0151_001 | -0.563 | 64.58 | | | | | | STI+aB0001_004 807 | TYR01A0023_001 | -0.881 | 50.72 1649 | GLU01A0056_001 | -1.9 | 999.00 1728 | VAL01A0059_001 | 0 | 45.68 2338 | THR01A0085_001 | 1.607 | 68.09 3322 | ARG01A0132_001 | 0.157 | 45.09 3699 | ASP01A0151_001 | -0.234 | 64.55 | | | STI+bB0001_006 807 | TYR01A0023_001 | -0.847 | 50.72 1649 | GLU01A0056_001 | -1.762 | 999.00 1728 | VAL01A0059_001 | 0 | 45.74 1849 | ILE01A0063_001 | 0 | 20.75 2338 | THR01A0085_001 | 1.56 | 68.09 3322 | ARG01A0132_001 | 0.27 | 45.06 3699 | ASP01A0151_001 | -0.532 | 64.56
ASP01A0151_001: ASP res 3 letter code, A chain ID, 0151 res number, 001 conf number. We also have vdw clashes in other complexes.