TY - CHAP AU - Bolton, E. E. AU - Wang, Y. AU - Thiessen, P. A. AU - Bryant, S. H. ED - Ralph, A. W. ED - David, C. S. PY - 2008 DA - 2008// TI - PubChem: integrated platform of small molecules and biological activities BT - Annual Reports in Computational Chemistry. Volume 4 PB - Elsevier CY - Amsterdam, the Netherlands UR - https://doi.org/10.1016/S1574-1400(08)00012-1 DO - 10.1016/S1574-1400(08)00012-1 ID - Bolton2008 ER - TY - JOUR AU - Wang, Y. L. AU - Xiao, J. W. AU - Suzek, T. O. AU - Zhang, J. AU - Wang, J. Y. AU - Bryant, S. H. PY - 2009 DA - 2009// TI - PubChem: a public information system for analyzing bioactivities of small molecules JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp456 DO - 10.1093/nar/gkp456 ID - Wang2009 ER - TY - JOUR AU - Wang, Y. L. AU - Bolton, E. AU - Dracheva, S. AU - Karapetyan, K. AU - Shoemaker, B. A. AU - Suzek, T. O. AU - Wang, J. Y. AU - Xiao, J. W. AU - Zhang, J. AU - Bryant, S. H. PY - 2010 DA - 2010// TI - An overview of the PubChem BioAssay resource JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp965 DO - 10.1093/nar/gkp965 ID - Wang2010 ER - TY - JOUR AU - Sayers, E. W. AU - Barrett, T. AU - Benson, D. A. AU - Bolton, E. AU - Bryant, S. H. AU - Canese, K. AU - Chetvernin, V. AU - Church, D. M. AU - DiCuccio, M. AU - Federhen, S. PY - 2011 DA - 2011// TI - Database resources of the National Center for Biotechnology Information JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1172 DO - 10.1093/nar/gkq1172 ID - Sayers2011 ER - TY - STD TI - PubChem substructure fingerprint description. [ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf] UR - ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf ID - ref5 ER - TY - JOUR AU - Chen, X. AU - Reynolds, C. H. PY - 2002 DA - 2002// TI - Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients JO - J Chem Inf Comput Sci VL - 42 UR - https://doi.org/10.1021/ci025531g DO - 10.1021/ci025531g ID - Chen2002 ER - TY - JOUR AU - Holliday, J. D. AU - Salim, N. AU - Whittle, M. AU - Willett, P. PY - 2003 DA - 2003// TI - Analysis and display of the size dependence of chemical similarity coefficients JO - J Chem Inf Comput Sci VL - 43 UR - https://doi.org/10.1021/ci034001x DO - 10.1021/ci034001x ID - Holliday2003 ER - TY - JOUR AU - Bolton, E. E. AU - Kim, S. AU - Bryant, S. H. PY - 2011 DA - 2011// TI - PubChem3D: similar conformers JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-13 DO - 10.1186/1758-2946-3-13 ID - Bolton2011 ER - TY - JOUR AU - Kim, S. AU - Bolton, E. E. AU - Bryant, S. H. PY - 2011 DA - 2011// TI - PubChem3D: biologically relevant 3-D similarity JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-26 DO - 10.1186/1758-2946-3-26 ID - Kim2011 ER - TY - JOUR AU - Bolton, E. E. AU - Chen, J. AU - Kim, S. AU - Han, L. AU - He, S. AU - Shi, W. AU - Simonyan, V. AU - Sun, Y. AU - Thiessen, P. A. AU - Wang, J. PY - 2011 DA - 2011// TI - PubChem3D: a new resource for scientists JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-32 DO - 10.1186/1758-2946-3-32 ID - Bolton2011 ER - TY - JOUR AU - Kim, S. AU - Bolton, E. AU - Bryant, S. PY - 2012 DA - 2012// TI - Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis JO - J Cheminform VL - 4 UR - https://doi.org/10.1186/1758-2946-4-28 DO - 10.1186/1758-2946-4-28 ID - Kim2012 ER - TY - STD TI - PubChem3D Thematic Series. [http://www.jcheminf.com/series/pubchem3d] UR - http://www.jcheminf.com/series/pubchem3d ID - ref12 ER - TY - JOUR AU - Bolton, E. E. AU - Kim, S. AU - Bryant, S. H. PY - 2011 DA - 2011// TI - PubChem3D: conformer generation JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-4 DO - 10.1186/1758-2946-3-4 ID - Bolton2011 ER - TY - JOUR AU - Kim, S. AU - Bolton, E. E. AU - Bryant, S. H. PY - 2011 DA - 2011// TI - PubChem3D: shape compatibility filtering using molecular shape quadrupoles JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-25 DO - 10.1186/1758-2946-3-25 ID - Kim2011 ER - TY - JOUR AU - Bolton, E. E. AU - Kim, S. AU - Bryant, S. H. PY - 2011 DA - 2011// TI - PubChem3D: diversity of shape JO - J Cheminform VL - 3 UR - https://doi.org/10.1186/1758-2946-3-9 DO - 10.1186/1758-2946-3-9 ID - Bolton2011 ER - TY - JOUR AU - Halgren, T. A. PY - 1996 DA - 1996// TI - Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94 JO - J Comput Chem VL - 17 UR - https://doi.org/3.0.CO;2-P DO - 3.0.CO;2-P ID - Halgren1996 ER - TY - JOUR AU - Halgren, T. A. PY - 1999 DA - 1999// TI - MMFF VI. MMFF94s option for energy minimization studies JO - J Comput Chem VL - 20 UR - https://doi.org/3.0.CO;2-X DO - 3.0.CO;2-X ID - Halgren1999 ER - TY - JOUR AU - Hawkins, P. C. D. AU - Skillman, A. G. AU - Warren, G. L. AU - Ellingson, B. A. AU - Stahl, M. T. PY - 2010 DA - 2010// TI - Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database JO - J Chem Inf Model VL - 50 UR - https://doi.org/10.1021/ci100031x DO - 10.1021/ci100031x ID - Hawkins2010 ER - TY - JOUR AU - Hawkins, P. C. D. AU - Nicholls, A. PY - 2012 DA - 2012// TI - Conformer Generation with OMEGA: learning from the data set and the analysis of failures JO - J Chem Inf Model VL - 52 UR - https://doi.org/10.1021/ci300314k DO - 10.1021/ci300314k ID - Hawkins2012 ER - TY - JOUR AU - Murrall, N. W. AU - Davies, E. K. PY - 1990 DA - 1990// TI - Conformational freedom in 3-D databases. 1. Techniques JO - J Chem Inf Comput Sci VL - 30 UR - https://doi.org/10.1021/ci00067a016 DO - 10.1021/ci00067a016 ID - Murrall1990 ER - TY - JOUR AU - Hurst, T. PY - 1994 DA - 1994// TI - Flexible 3D searching: the directed tweak technique JO - J Chem Inf Comput Sci VL - 34 UR - https://doi.org/10.1021/ci00017a025 DO - 10.1021/ci00017a025 ID - Hurst1994 ER - TY - JOUR AU - Klebe, G. AU - Mietzner, T. PY - 1994 DA - 1994// TI - A fast and efficient method to generate biologically relevant conformations JO - J Comput Aided Mol Des VL - 8 UR - https://doi.org/10.1007/BF00123667 DO - 10.1007/BF00123667 ID - Klebe1994 ER - TY - JOUR AU - Renner, S. AU - Schwab, C. H. AU - Gasteiger, J. AU - Schneider, G. PY - 2006 DA - 2006// TI - Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors JO - J Chem Inf Model VL - 46 UR - https://doi.org/10.1021/ci050075s DO - 10.1021/ci050075s ID - Renner2006 ER - TY - JOUR AU - Greene, J. AU - Kahn, S. AU - Savoj, H. AU - Sprague, P. AU - Teig, S. PY - 1994 DA - 1994// TI - Chemical function queries for 3D database search JO - J Chem Inf Comput Sci VL - 34 UR - https://doi.org/10.1021/ci00022a012 DO - 10.1021/ci00022a012 ID - Greene1994 ER - TY - STD TI - OMEGA, Version 2.1. 2006, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref25 ER - TY - STD TI - OMEGA, Version 2.2. 2007, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref26 ER - TY - STD TI - OMEGA, Version 2.3. 2008, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref27 ER - TY - STD TI - OMEGA, Version 2.4. 2009, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref28 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 - Borodina, Y. V. AU - Bolton, E. AU - Fontaine, F. AU - Bryant, S. H. PY - 2007 DA - 2007// TI - Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space JO - J Chem Inf Model VL - 47 UR - https://doi.org/10.1021/ci7000956 DO - 10.1021/ci7000956 ID - Borodina2007 ER - TY - JOUR AU - Madej, T. AU - Addess, K. J. AU - Fong, J. H. AU - Geer, L. Y. AU - Geer, R. C. AU - Lanczycki, C. J. AU - Liu, C. L. AU - Lu, S. N. AU - Marchler-Bauer, A. AU - Panchenko, A. R. PY - 2012 DA - 2012// TI - MMDB: 3D structures and macromolecular interactions JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1162 DO - 10.1093/nar/gkr1162 ID - Madej2012 ER - TY - JOUR AU - Bostrom, J. PY - 2001 DA - 2001// TI - Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools JO - J Comput Aided Mol Des VL - 15 UR - https://doi.org/10.1023/A:1015930826903 DO - 10.1023/A:1015930826903 ID - Bostrom2001 ER - TY - JOUR AU - Nicklaus, M. C. AU - Wang, S. M. AU - Driscoll, J. S. AU - Milne, G. W. A. PY - 1995 DA - 1995// TI - Conformational changes of small molecules binding to proteins JO - Bioorg Med Chem VL - 3 UR - https://doi.org/10.1016/0968-0896(95)00031-B DO - 10.1016/0968-0896(95)00031-B ID - Nicklaus1995 ER - TY - JOUR AU - Nissink, J. W. M. AU - Murray, C. AU - Hartshorn, M. AU - Verdonk, M. L. AU - Cole, J. C. AU - Taylor, R. PY - 2002 DA - 2002// TI - A new test set for validating predictions of protein-ligand interaction JO - Proteins-Structure Function and Genetics VL - 49 UR - https://doi.org/10.1002/prot.10232 DO - 10.1002/prot.10232 ID - Nissink2002 ER - TY - CHAP AU - Westbrook, J. AU - Feng, Z. K. AU - Burkhardt, K. AU - Berman, H. M. PY - 2003 DA - 2003// TI - Validation of protein structures for Protein Data Bank BT - Macromolecular Crystallography, Pt D PB - Academic Press Inc CY - San Diego UR - https://doi.org/10.1016/S0076-6879(03)74017-8 DO - 10.1016/S0076-6879(03)74017-8 ID - Westbrook2003 ER - TY - JOUR AU - Acharya, K. R. AU - Lloyd, M. D. PY - 2005 DA - 2005// TI - The advantages and limitations of protein crystal structures JO - Trends Pharmacol Sci VL - 26 UR - https://doi.org/10.1016/j.tips.2004.10.011 DO - 10.1016/j.tips.2004.10.011 ID - Acharya2005 ER - TY - STD TI - ROCS - Rapid Overlay of Chemical Structures, Version 3.1.0. 2010, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref37 ER - TY - STD TI - ShapeTK - C++, Version 1.8.0. 2010, OpenEye Scientific Software, Inc, Santa Fe, NM ID - ref38 ER - TY - JOUR AU - Grant, J. A. AU - Gallardo, M. A. AU - Pickup, B. T. PY - 1996 DA - 1996// TI - A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape JO - J Comput Chem VL - 17 UR - https://doi.org/3.0.CO;2-K DO - 3.0.CO;2-K ID - Grant1996 ER - TY - JOUR AU - Rush, T. S. AU - Grant, J. A. AU - Mosyak, L. AU - Nicholls, A. PY - 2005 DA - 2005// TI - A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction JO - J Med Chem VL - 48 UR - https://doi.org/10.1021/jm040163o DO - 10.1021/jm040163o ID - Rush2005 ER - TY - JOUR AU - Cruickshank, D. W. J. PY - 1999 DA - 1999// TI - Remarks about protein structure precision JO - Acta Crystallogr D VL - 55 UR - https://doi.org/10.1107/S0907444998012645 DO - 10.1107/S0907444998012645 ID - Cruickshank1999 ER - TY - JOUR AU - Cruickshank, D. W. J. PY - 1999 DA - 1999// TI - Remarks about protein structure precision (vol 55, pg 583, 1999) JO - Acta Crystallogr D VL - 55 UR - https://doi.org/10.1107/S0907444999004308 DO - 10.1107/S0907444999004308 ID - Cruickshank1999 ER - TY - JOUR AU - Blow, D. M. PY - 2002 DA - 2002// TI - Rearrangement of Cruickshank’s formulae for the diffraction-component precision index JO - Acta Crystallogr D VL - 58 UR - https://doi.org/10.1107/S0907444902003931 DO - 10.1107/S0907444902003931 ID - Blow2002 ER - TY - JOUR AU - Goto, J. AU - Kataoka, R. AU - Hirayama, N. PY - 2004 DA - 2004// TI - Ph4Dock: pharmacophore-based protein-ligand docking JO - J Med Chem VL - 47 UR - https://doi.org/10.1021/jm0493818 DO - 10.1021/jm0493818 ID - Goto2004 ER - TY - JOUR AU - Chen, J. AU - Anderson, J. B. AU - DeWeese-Scott, C. AU - Fedorova, N. D. AU - Geer, L. Y. AU - He, S. AU - Hurwitz, D. I. AU - Jackson, J. D. AU - Jacobs, A. R. AU - Lanczycki, C. J. PY - 2003 DA - 2003// TI - MMDB: Entrez’s 3D-structure database JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg086 DO - 10.1093/nar/gkg086 ID - Chen2003 ER - TY - JOUR AU - Wang, Y. AU - Addess, K. J. AU - Chen, J. AU - Geer, L. Y. AU - He, J. AU - He, S. AU - Lu, S. AU - Madej, T. AU - Marchler-Bauer, A. AU - Thiessen, P. A. PY - 2007 DA - 2007// TI - MMDB: annotating protein sequences with Entrez’s 3D-structure database JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl952 DO - 10.1093/nar/gkl952 ID - Wang2007 ER - TY - JOUR AU - Murshudov, G. N. AU - Vagin, A. A. AU - Dodson, E. J. PY - 1997 DA - 1997// TI - Refinement of macromolecular structures by the maximum-likelihood method JO - Acta Crystallogr D VL - 53 UR - https://doi.org/10.1107/S0907444996012255 DO - 10.1107/S0907444996012255 ID - Murshudov1997 ER - TY - JOUR AU - Jones, T. A. AU - Zou, J. Y. AU - Cowan, S. W. AU - Kjeldgaard, M. PY - 1991 DA - 1991// TI - Improved methods for building protein models in electron-density maps and the location of errors in these models JO - Acta Crystallogr A VL - 47 UR - https://doi.org/10.1107/S0108767390010224 DO - 10.1107/S0108767390010224 ID - Jones1991 ER - TY - JOUR AU - Kleywegt, G. J. AU - Harris, M. R. AU - Zou, J. Y. AU - Taylor, T. C. AU - Wahlby, A. AU - Jones, T. A. PY - 2004 DA - 2004// TI - The Uppsala electron-density server JO - Acta Crystallogr D VL - 60 UR - https://doi.org/10.1107/S0907444904013253 DO - 10.1107/S0907444904013253 ID - Kleywegt2004 ER - TY - STD TI - Electron Density Server (EDS). [http://www.jcheminf.com/series/pubchem3d] UR - http://www.jcheminf.com/series/pubchem3d ID - ref50 ER - TY - JOUR AU - Grant, J. A. AU - Haigh, J. A. AU - Pickup, B. T. AU - Nicholls, A. AU - Sayle, R. A. PY - 2006 DA - 2006// TI - Lingos, finite state machines, and fast similarity searching JO - J Chem Inf Model VL - 46 UR - https://doi.org/10.1021/ci6002152 DO - 10.1021/ci6002152 ID - Grant2006 ER - TY - JOUR AU - Bostrom, J. AU - Greenwood, J. R. AU - Gottfries, J. PY - 2003 DA - 2003// TI - Assessing the performance of OMEGA with respect to retrieving bioactive conformations JO - J Mol Graph Model VL - 21 UR - https://doi.org/10.1016/S1093-3263(02)00204-8 DO - 10.1016/S1093-3263(02)00204-8 ID - Bostrom2003 ER - TY - JOUR AU - Scior, T. AU - Bender, A. AU - Tresadern, G. AU - Medina-Franco, J. L. AU - Martinez-Mayorga, K. AU - Langer, T. AU - Cuanalo-Contreras, K. AU - Agrafiotis, D. K. PY - 2012 DA - 2012// TI - Recognizing pitfalls in virtual screening: a critical review JO - J Chem Inf Model VL - 52 UR - https://doi.org/10.1021/ci200528d DO - 10.1021/ci200528d ID - Scior2012 ER -