TY - JOUR AU - Berman, H. AU - Henrick, K. AU - Nakamura, H. AU - Markley, J. L. PY - 2007 DA - 2007// TI - The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl971 DO - 10.1093/nar/gkl971 ID - Berman2007 ER - TY - JOUR AU - Spek, A. L. PY - 2009 DA - 2009// TI - Structure validation in chemical crystallography JO - Acta Crystallogr D VL - 65 UR - https://doi.org/10.1107/S090744490804362X DO - 10.1107/S090744490804362X ID - Spek2009 ER - TY - JOUR AU - Yang, L. W. AU - Eyal, E. AU - Chennubhotla, C. AU - Jee, J. G. AU - Gronenborn, A. M. AU - Bahar, I. PY - 2007 DA - 2007// TI - Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions JO - Structure VL - 15 UR - https://doi.org/10.1016/j.str.2007.04.014 DO - 10.1016/j.str.2007.04.014 ID - Yang2007 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. AU - Shindyalov, I. N. AU - Bourne, P. E. PY - 2000 DA - 2000// TI - The protein data bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Dehof, A. K. AU - Rurainski, A. AU - Bui, Q. B. A. AU - Bocker, S. AU - Lenhof, H. P. AU - Hildebrandt, A. PY - 2011 DA - 2011// TI - Automated bond order assignment as an optimization problem JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btq718 DO - 10.1093/bioinformatics/btq718 ID - Dehof2011 ER - TY - JOUR AU - Baber, J. C. AU - Hodgkin, E. E. PY - 1992 DA - 1992// TI - Automatic assignment of chemical connectivity to organic molecules in the Cambridge structural database JO - J Chem Inf Comput Sci VL - 32 UR - https://doi.org/10.1021/ci00009a001 DO - 10.1021/ci00009a001 ID - Baber1992 ER - TY - JOUR AU - Bruno, I. J. AU - Shields, G. P. AU - Taylor, R. PY - 2011 DA - 2011// TI - Deducing chemical structure from crystallographically determined atomic coordinates JO - Acta Crystallogr B VL - 67 UR - https://doi.org/10.1107/S0108768111024608 DO - 10.1107/S0108768111024608 ID - Bruno2011 ER - TY - JOUR AU - Froeyen, M. AU - Herdewijn, P. PY - 2005 DA - 2005// TI - Correct bond order assignment in a molecular framework using integer linear programming with application to molecules where only non-hydrogen atom coordinates are available JO - J Chem Inf Comput Model VL - 45 UR - https://doi.org/10.1021/ci049645z DO - 10.1021/ci049645z ID - Froeyen2005 ER - TY - JOUR AU - Hendlich, M. AU - Rippmann, F. AU - Barnickel, G. PY - 1997 DA - 1997// TI - BALI: automatic assignment of bond and atom types for protein ligands in the brookhaven protein databank JO - J Chem Inf Comput Sci VL - 37 UR - https://doi.org/10.1021/ci9603487 DO - 10.1021/ci9603487 ID - Hendlich1997 ER - TY - JOUR AU - Labute, P. PY - 2005 DA - 2005// TI - On the perception of molecules from 3D atomic coordinates JO - J Chem Inf Comput Model VL - 45 UR - https://doi.org/10.1021/ci049915d DO - 10.1021/ci049915d ID - Labute2005 ER - TY - JOUR AU - Meng, E. C. AU - Lewis, R. A. PY - 1991 DA - 1991// TI - Determination of molecular topology and atomic hybridization states from heavy atom coordinates JO - J Comput Chem VL - 12 UR - https://doi.org/10.1002/jcc.540120716 DO - 10.1002/jcc.540120716 ID - Meng1991 ER - TY - CHAP AU - Sayle, R. PY - 2001 DA - 2001// TI - PDB: Cruft to content (Perception of molecular connectivity from 3D coordinates) BT - Daylight user meeting MUG01 ID - Sayle2001 ER - TY - JOUR AU - Zhao, Y. AU - Cheng, T. AU - Wang, R. PY - 2007 DA - 2007// TI - Automatic perception of organic molecules based on essential structural information JO - J Chem Inf Comput Model VL - 47 UR - https://doi.org/10.1021/ci700028w DO - 10.1021/ci700028w ID - Zhao2007 ER - TY - JOUR AU - Wang, J. M. AU - Wang, W. AU - Kollman, P. A. AU - Case, D. A. PY - 2006 DA - 2006// TI - Automatic atom type and bond type perception in molecular mechanical calculations JO - J Mol Graph Model VL - 25 UR - https://doi.org/10.1016/j.jmgm.2005.12.005 DO - 10.1016/j.jmgm.2005.12.005 ID - Wang2006 ER - TY - JOUR AU - Ricketts, E. M. AU - Bradshaw, J. AU - Hann, M. AU - Hayes, F. AU - Tanna, N. AU - Ricketts, D. M. PY - 1993 DA - 1993// TI - Comparison of conformations of small molecule structures from the protein data bank with those generated by Concord, Cobra, ChemDBS-3D, and converter and those extracted from the Cambridge structural database JO - J Chem Inf Comput Sci VL - 33 UR - https://doi.org/10.1021/ci00016a013 DO - 10.1021/ci00016a013 ID - Ricketts1993 ER - TY - STD TI - Discovery Studio 2.5 Guide, Accelrys Inc., San Diego. 2009, http://www.accelrys.com, UR - http://www.accelrys.com ID - ref16 ER - TY - STD TI - SYBYL-X 1.3 molecular simulation package. 2011, St. Louis, http://www.sybyl.com, UR - http://www.sybyl.com ID - ref17 ER - TY - JOUR AU - Hou, T. J. AU - Xia, K. AU - Zhang, W. AU - Xu, X. J. PY - 2004a DA - 2004a// TI - ADME evaluation in drug discovery. 4. Prediction of aqueous solubility based on atom contribution approach JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci034184n DO - 10.1021/ci034184n ID - Hou2004a ER - TY - STD TI - MOE, Chemical Computing Group Inc: 2011, Montreal, Canada, http://www.chemcomp.com/. 2011, UR - http://www.chemcomp.com/ ID - ref19 ER - TY - JOUR AU - Allen, F. H. PY - 2002 DA - 2002// TI - The Cambridge structural database: a quarter of a million crystal structures and rising JO - Acta Crystallogr B VL - 58 UR - https://doi.org/10.1107/S0108768102003890 DO - 10.1107/S0108768102003890 ID - Allen2002 ER - TY - JOUR AU - Irwin, J. J. AU - Shoichet, B. K. PY - 2005 DA - 2005// TI - ZINC-a free database of commercially available compounds for virtual screening JO - J Chem Inf Comput Model VL - 45 UR - https://doi.org/10.1021/ci049714+ DO - 10.1021/ci049714+ ID - Irwin2005 ER -