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title = {{Identification of a chemical probe for {NAADP} by virtual screening}},  journal = {Nature Chemical Biology},  }  @article{Nicholls2010,  author = {A. Nicholls and G. B. McGaughey and R. P. Sheridan and  A. C. Good and G. Warren and M. Mathieu and  S. W. Muchmore and S. P. Brown and J. A. Grant and  J. A. Haigh},  journal = {J Med Chem},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/20158188}{20158188}]  [PubMed  Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874267}{PMC2874267}]  [doi:\href{http://dx.doi.org/10.1021/jm900818s}{10.1021/jm900818s}]},  number = {10},  pages = {3862},  publisher = {American Chemical Society},  title = {{Molecular shape and medicinal chemistry: a  perspective}},  volume = {53},  year = {2010},  }  @article{RushIII2005,  author = {T. S. {Rush III} and J. A. Grant and L. Mosyak and  A. Nicholls},  journal = {J Med Chem},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15743191}{15743191}]  [doi:\href{http://dx.doi.org/10.1021/jm040163o}{10.1021/jm040163o}]},  number = {5},  pages = {1489--1495},  publisher = {ACS Publications},  title = {{A shape-based 3-D scaffold hopping method and its  application to a bacterial protein-protein  interaction}},  volume = {48},  year = {2005},  issn = {0022-2623},  }  @article{McMasters2009,  author = {D. R. McMasters and M. Garcia-Calvo and V. Maiorov and  M. E. McCann and R. D. Meurer and H. G. Bull and  J. M. Lisnock and K. L. Howell and R. J. DeVita},  journal = {Bioorganic \& medicinal chemistry letters},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19410454}{19410454}]  [doi:\href{http://dx.doi.org/10.1016/j.bmcl.2009.04.031}{10.1016/j.bmcl.2009.04.031}]},  number = {11},  pages = {2965--2968},  publisher = {Elsevier},  title = {{Spiroimidazolidinone NPC1L1 inhibitors. 1: Discovery  by 3D-similarity-based virtual screening}},  volume = {19},  year = {2009},  issn = {0960-894X},  }  @article{Muchmore2006,  author = {S. W. Muchmore and A. J. Souers and  I. Akritopoulou-Zanze},  journal = {Chemical biology \& drug design},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/16492165}{16492165}]  [doi:\href{http://dx.doi.org/10.1111/j.1747-0285.2006.00341.x}{10.1111/j.1747-0285.2006.00341.x}]},  number = {2},  pages = {174--176},  publisher = {Wiley Online Library},  title = {{The Use of Three-Dimensional Shape and Electrostatic  Similarity Searching in the Identification of a  Melanin{\^a}Concentrating Hormone Receptor 1  Antagonist}},  volume = {67},  year = {2006},  issn = {1747-0285},  }  @article{Rees2004,  author = {D. C. Rees and M. Congreve and C. W. Murray and  R. Carr},  journal = {Nature Reviews Drug Discovery},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15286733}{15286733}]  [doi:\href{http://dx.doi.org/10.1038/nrd1467}{10.1038/nrd1467}]},  number = {8},  pages = {660--672},  publisher = {Nature Publishing Group},  title = {{Fragment-based lead discovery}},  volume = {3},  year = {2004},  }  @article{Congreve2008,  author = {Miles Congreve and Gianni Chessari and Dominic Tisi and  Andrew J. Woodhead},  journal = {J Med Chem},  month = {May},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/18457385}{18457385}]  [doi:\href{http://dx.doi.org/10.1021/jm8000373}{10.1021/jm8000373}]},  number = {13},  pages = {3661--3680},  publisher = {American Chemical Society},  title = {{Recent Developments in Fragment-Based Drug  Discovery}},  volume = {51},  year = {2008},  issn = {0022-2623},  }  @article{Ebalunode2008,  author = {Jerry Osagie Ebalunode and Zheng Ouyang and Jie Liang and  Weifan Zheng},  journal = {J. Chem. Inf. Model.},  month = {Apr},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/18396858}{18396858}]  [doi:\href{http://dx.doi.org/10.1021/ci700368p}{10.1021/ci700368p}]},  number = {4},  pages = {889--901},  publisher = {American Chemical Society},  title = {{Novel Approach to Structure-Based Pharmacophore  Search Using Computational Geometry and Shape  Matching Techniques}},  volume = {48},  year = {2008},  abstract = {Computationally efficient structure-based virtual  screening methods have recently been reported that  seek to find effective means to utilize experimental  structure information without employing detailed  molecular docking calculations. These tools can be  coupled with efficient experimental screening  technologies to improve the probability of  identifying hits and leads for drug discovery  research. Commercial software ROCS (rapid overlay of  chemical structures) from Open Eye Scientific is such  an example, which is a shape-based virtual screening  method using the 3D structure of a ligand, typically  from a bound X-ray costructure, as the query. We  report here the development of a new structure-based  pharmacophore search method (called Shape4) for  virtual screening. This method adopts a variant of  the ROCS shape technology and expands its use to work  with an empty crystal structure. It employs a  rigorous computational geometry method and a  deterministic geometric casting algorithm to derive  the negative image (i.e., pseudoligand) of a target  binding site. Once the negative image (or  pseudoligand) is generated, an efficient shape  comparison algorithm in the commercial OE SHAPE  Toolkit is adopted to compare and match small organic  molecules with the shape of the pseudoligand. We  report the detailed computational protocol and its  computational validation using known biologically  active compounds extracted from the WOMBAT database.  Models derived for five selected targets were used to  perform the virtual screening experiments to obtain  the enrichment data for various virtual screening  methods. It was found that our approach afforded  similar or better enrichment ratios than other  related methods, often with better diversity among  the top ranking computational hits.},  issn = {1549-9596},  }  @article{Vainio2009,  author = {M. J. Vainio and J. S. Puranen and M. S. Johnson},  journal = {Journal of chemical information and modeling},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19434847}{19434847}]  [doi:\href{http://dx.doi.org/10.1021/ci800315d}{10.1021/ci800315d}]},  number = {2},  pages = {492--502},  publisher = {ACS Publications},  title = {{ShaEP: molecular overlay based on shape and  electrostatic potential}},  volume = {49},  year = {2009},  issn = {1549-9596},  }  @article{Cheeseright2006,  author = {T. Cheeseright and M. Mackey and S. Rose and  A. Vinter},  journal = {Journal of chemical information and modeling},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/16562997}{16562997}]  [doi:\href{http://dx.doi.org/10.1021/ci050357s}{10.1021/ci050357s}]},  number = {2},  pages = {665--676},  publisher = {ACS Publications},  title = {{Molecular field extrema as descriptors of biological  activity: definition and validation}},  volume = {46},  year = {2006},  issn = {1549-9596},  }  @article{Thorner1996,  author = {D. A. Thorner and D. J. Wild and P. Willett and  P. M. Wright},  journal = {J. Chem. Inf. Comput. Sci},  note =  {[doi:\href{http://dx.doi.org/10.1021/ci960002w}{10.1021/ci960002w}]},  number = {4},  pages = {900--908},  title = {{Similarity searching in files of three-dimensional  chemical structures: flexible field-based searching  of molecular electrostatic potentials}},  volume = {36},  year = {1996},  }  @article{Tervo2005,  author = {A. J. Tervo and T. R\"onkk\"o and T. H. Nyr\"onen and  A. Poso},  journal = {Journal of medicinal chemistry},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15943481}{15943481}]  [doi:\href{http://dx.doi.org/10.1021/jm049123a}{10.1021/jm049123a}]},  number = {12},  pages = {4076--4086},  publisher = {ACS Publications},  title = {{BRUTUS: optimization of a grid-based similarity  function for rigid-body molecular superposition. 1.  Alignment and virtual screening applications}},  volume = {48},  year = {2005},  issn = {0022-2623},  }  @article{Marin2008,  author = {R. M. Mar\'i-n and N. F. Aguirre and E. E. Daza},  journal = {Journal of chemical information and modeling},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/18166018}{18166018}]  [doi:\href{http://dx.doi.org/10.1021/ci7001878}{10.1021/ci7001878}]},  number = {1},  pages = {109--118},  publisher = {ACS Publications},  title = {{Graph theoretical similarity approach to compare  molecular electrostatic potentials}},  volume = {48},  year = {2008},  issn = {1549-9596},  }  @article{Sastry2011,  author = {M. Sastry and S. Dixon and W. Sherman},  journal = {J. Chem. Inf. Model.},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/21870862}{21870862}]  [doi:\href{http://dx.doi.org/10.1021/ci2002704}{10.1021/ci2002704}]},  publisher = {ACS Publications},  title = {{Rapid Shape-Based Ligand Alignment and Virtual  Screening Method Based on Atom/Feature-Pair  Similarities and Volume Overlap Scoring}},  year = {2011},  issn = {1549-9596},  }  @article{Good1993,  author = {A. C. Good and W. G. Richards},  journal = {J. Chem. Inf. Model.},  number = {1},  pages = {112--116},  publisher = {American Chemical Society},  title = {{Rapid evaluation of shape similarity using Gaussian  functions}},  volume = {33},  year = {1993},  abstract = {Uses gaussian function (approximating electron  fields) to analytically calculate carbo index (amount  of overlap) between two already aligned molecules.  The analytical method is faster than a fine grained  grid method.},  }  @article{Grant1996,  author = {J. A. Grant and M. A. Gallardo and B. T. Pickup},  journal = {Journal of Computational Chemistry},  number = {14},  pages = {1653--1666},  publisher = {John Wiley \& Sons},  title = {{A fast method of molecular shape comparison: A  simple application of a Gaussian description of  molecular shape}},  volume = {17},  year = {1996},  }  @article{Proschak2008,  author = {Ewgenij Proschak and Matthias Rupp and  Swetlana Derksen and Gisbert Schneider},  journal = {Journal of Computational Chemistry},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/17516427}{17516427}]  [doi:\href{http://dx.doi.org/10.1002/jcc.20770}{10.1002/jcc.20770}]},  number = {1},  pages = {108--114},  publisher = {Wiley Subscription Services, Inc., A Wiley Company},  title = {{Shapelets: Possibilities and limitations of  shape-based virtual screening}},  volume = {29},  year = {2008},  abstract = {Complementarity of molecular surfaces is crucial for  molecular recognition. A method for representation of  molecular shape is presented. We decompose the  molecular surface into commensurate patches with  defined shape by fitting hyperbolical paraboloids  onto a triangulated isosurface of the Gaussian model  of a molecule. As a result of this decomposition we  obtain a 3D graph representation of the molecular  shape, which can be used for complete and partial  shape matching and isosteric group searching. To  point out the possibilities and limitations of  shape-only models, we challenged our method by three  scenarios in a virtual screening contest: rigid body  alignment, consensus shape filtering, and  target-specific screening. {\^A}\textcopyright 2007  Wiley Periodicals, Inc. J Comput Chem, 2008},  issn = {1096-987X},  }  @article{Fontaine2007,  author = {F. Fontaine and E. Bolton and Y. Borodina and  S. H. Bryant},  journal = {Chemistry Central Journal},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/17880744}{17880744}]  [PubMed  Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994057}{PMC1994057}]  [doi:\href{http://dx.doi.org/10.1186/1752-153X-1-12}{10.1186/1752-153X-1-12}]},  pages = {12},  publisher = {BioMed Central},  title = {{Fast 3D shape screening of large chemical databases  through alignment-recycling}},  volume = {1},  year = {2007},  }  @article{Haigh2005,  author = {J. A. Haigh and B. T. Pickup and J. A. Grant and  A. Nicholls},  journal = {J. Chem. Inf. Model},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15921457}{15921457}]  [doi:\href{http://dx.doi.org/10.1021/ci049651v}{10.1021/ci049651v}]},  number = {3},  pages = {673--684},  publisher = {ACS Publications},  title = {{Small molecule shape-fingerprints}},  volume = {45},  year = {2005},  }  @article{Putta2002,  author = {S. Putta and C. Lemmen and P. Beroza and J. Greene},  journal = {J. Chem. Inf. Comput. Sci},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/12377013}{12377013}]},  number = {5},  pages = {1230--1240},  title = {{A novel shape-feature based approach to virtual  library screening}},  volume = {42},  year = {2002},  }  @article{Ballester2007,  author = {P. J. Ballester and W. G. Richards},  journal = {J. Comp. Chem.},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/17342716}{17342716}]  [doi:\href{http://dx.doi.org/10.1002/jcc.20681}{10.1002/jcc.20681}]},  number = {10},  pages = {1711},  publisher = {John Wiley \& Sons, Ltd},  title = {{Ultrafast shape recognition to search compound  databases for similar molecular shapes}},  volume = {28},  year = {2007},  }  @article{Zauhar2003,  author = {R. J. Zauhar and G. Moyna and L. F. Tian and Z. J. Li and  W. J. Welsh},  journal = {J. Med. Chem},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/14667221}{14667221}]  [doi:\href{http://dx.doi.org/10.1021/jm030242k}{10.1021/jm030242k}]},  number = {26},  pages = {5674--5690},  title = {{Shape signatures: a new approach to computer-aided  ligand-and receptor-based drug design}},  volume = {46},  year = {2003},  }  @article{Schneider2005,  author = {Gisbert Schneider and Uli Fechner},  journal = {Nat Rev Drug Discov},  month = {Aug},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/16056391}{16056391}]  [doi:\href{http://dx.doi.org/10.1038/nrd1799}{10.1038/nrd1799}]},  number = {8},  pages = {649--663},  title = {{Computer-based de novo design of drug-like  molecules}},  volume = {4},  year = {2005},  issn = {1474-1776},  url = {http://dx.doi.org/10.1038/nrd1799},  }  @article{Kick1997,  author = {E. K. Kick and D. C. Roe and A. {Geoffrey Skillman} and  G. Liu and T. J. A. Ewing and Y. Sun and I. D. Kuntz and  J. A. Ellman},  journal = {Chemistry \& Biology},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/9195867}{9195867}]},  number = {4},  pages = {297--307},  publisher = {Elsevier},  title = {{Structure-based design and combinatorial chemistry  yield low nanomolar inhibitors of cathepsin D}},  volume = {4},  year = {1997},  }  @article{Murray1997,  author = {C. W. Murray and D. E. Clark and T. R. Auton and  M. A. Firth and J. Li and R. A. Sykes and  B. Waszkowycz and D. R. Westhead and S. C. Young},  journal = {J Comput Aided Mol Des},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/9089436}{9089436}]},  number = {2},  pages = {193--207},  publisher = {Springer},  title = {{PRO\_SELECT: combining structure-based drug design  and combinatorial chemistry for rapid lead discovery.  1. Technology}},  volume = {11},  year = {1997},  }  @article{Li1998,  author = {J. Li and C. W. Murray and B. Waszkowycz and  S. C. Young},  journal = {Drug discovery today},  number = {3},  pages = {105--112},  publisher = {Elsevier},  title = {{Targeted molecular diversity in drug discovery:  integration of structure-based design and  combinatorial chemistry}},  volume = {3},  year = {1998},  issn = {1359-6446},  }  @article{Liebeschuetz2002,  author = {J. W. Liebeschuetz and S. D. Jones and P. J. Morgan and  C. W. Murray and A. D. Rimmer and J. M. E. Roscoe and  B. Waszkowycz and P. M. Welsh and W. A. Wylie and  S. C. Young},  journal = {Journal of medicinal chemistry},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/11881991}{11881991}]},  number = {6},  pages = {1221--1232},  publisher = {ACS Publications},  title = {{PRO\_SELECT: combining structure-based drug design  and array-based chemistry for rapid lead discovery.  2. The development of a series of highly potent and  selective factor Xa inhibitors}},  volume = {45},  year = {2002},  issn = {0022-2623},  }  @article{Brenke2009,  author = {R. Brenke and D. Kozakov and G. Y. Chuang and  D. Beglov and D. Hall and M. R. Landon and C. Mattos and  S. Vajda},  journal = {Bioinformatics},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19176554}{19176554}]  [PubMed  Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647826}{PMC2647826}]  [doi:\href{http://dx.doi.org/10.1093/bioinformatics/btp036}{10.1093/bioinformatics/btp036}]},  number = {5},  pages = {621},  publisher = {Oxford Univ Press},  title = {{Fragment-based identification of druggable hot spots  of proteins using Fourier domain correlation  techniques}},  volume = {25},  year = {2009},  issn = {1367-4803},  }  @article{Bronstein2009,  author = {A. M. Bronstein and M. M. Bronstein and  A. M. Bruckstein and R. Kimmel},  journal = {International Journal of Computer Vision},  number = {2},  pages = {163--183},  publisher = {Springer},  title = {{Partial similarity of objects, or how to compare a  centaur to a horse}},  volume = {84},  year = {2009},  issn = {0920-5691},  }  @article{Zhang2009,  author = {J. Zhang and S. Smith},  journal = {Journal of Computing and Information Science in  Engineering},  pages = {034503},  title = {{Shape Similarity Matching With Octree  Representations}},  volume = {9},  year = {2009},  }  @inproceedings{keim1999,  address = {New York, NY, USA},  author = {Daniel A. Keim},  booktitle = {{Proc. of the Intl. Conf. on Management of Data}},  pages = {419--430},  publisher = {ACM},  title = {{Efficient geometry-based similarity search of 3D  spatial databases}},  year = {1999},  doi = {10.1145/304182.304219},  isbn = {1-58113-084-8},  url = {http://doi.acm.org/10.1145/304182.304219},  }  @article{Rohrer2009,  author = {S. G. Rohrer and K. Baumann},  journal = {J Chem Inf Model},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19434821}{19434821}]  [doi:\href{http://dx.doi.org/10.1021/ci8002649}{10.1021/ci8002649}]},  number = {2},  pages = {169--84},  title = {{Maximum unbiased validation (MUV) data sets for  virtual screening based on PubChem bioactivity data}},  volume = {49},  year = {2009},  abstract = {Refined nearest neighbor analysis was recently  introduced for the analysis of virtual screening  benchmark data sets. It constitutes a technique from  the field of spatial statistics and provides a  mathematical framework for the nonparametric analysis  of mapped point patterns. Here, refined nearest  neighbor analysis is used to design benchmark data  sets for virtual screening based on PubChem  bioactivity data. A workflow is devised that purges  data sets of compounds active against  pharmaceutically relevant targets from unselective  hits. Topological optimization using experimental  design strategies monitored by refined nearest  neighbor analysis functions is applied to generate  corresponding data sets of actives and decoys that  are unbiased with regard to analogue bias and  artificial enrichment. These data sets provide a tool  for Maximum Unbiased Validation (MUV) of virtual  screening methods. The data sets and a software  package implementing the MUV design workflow are  freely available at  http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html.},  }  @article{Good2008,  author = {A. C. Good and T. I. Oprea},  journal = {Journal of computer-aided molecular design},  number = {3},  pages = {169--178},  publisher = {Springer},  title = {{Optimization of CAMD techniques 3. Virtual screening  enrichment studies: a help or hindrance in tool  selection?}},  volume = {22},  year = {2008},  issn = {0920-654X},  }  @article{Verdonk2004,  author = {M. L. Verdonk and V. Berdini and M. J. Hartshorn and  W. T. Mooij and C. W. Murray and R. D. Taylor and  P. Watson},  journal = {Journal of chemical information and computer  sciences},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15154744}{15154744}]  [doi:\href{http://dx.doi.org/10.1021/ci034289q}{10.1021/ci034289q}]},  number = {3},  pages = {793},  title = {{Virtual screening using protein-ligand docking:  avoiding artificial enrichment.}},  volume = {44},  year = {2004},  }  @article{Anstead1997,  author = {G. M. Anstead and K. E. Carlson and  J. A. Katzenellenbogen},  journal = {Steroids},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/9071738}{9071738}]},  number = {3},  pages = {268--303},  publisher = {Elsevier},  title = {{The estradiol pharmacophore: ligand  structure-estrogen receptor binding affinity  relationships and a model for the receptor binding  site}},  volume = {62},  year = {1997},  issn = {0039-128X},  }  @article{Tiikkainen2009,  author = {Pekka Tiikkainen and Patrick Markt and Gerhard Wolber and  Johannes Kirchmair and Simona Distinto and Antti Poso and  Olli Kallioniemi},  journal = {Journal of Chemical Information and Modeling},  month = {Oct},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/19799417}{19799417}]  [doi:\href{http://dx.doi.org/10.1021/ci900249b}{10.1021/ci900249b}]},  number = {10},  pages = {2168--2178},  publisher = {American Chemical Society},  title = {{Critical Comparison of Virtual Screening Methods  against the MUV Data Set}},  volume = {49},  year = {2009},  abstract = {In the current work, we measure the performance of  seven ligand-based virtual screening tools - five  similarity search methods and two pharmacophore  elucidators - against the MUV data set. For the  similarity search tools, single active molecules as  well as active compound sets clustered in terms of  their chemical diversity were used as templates.  Their score was calculated against all inactive and  active compounds in their target class. Subsequently,  the scores were used to calculate different  performance metrics including enrichment factors and  AUC values. We also studied the effect of data fusion  on the results. To measure the performance of the  pharmacophore tools, a set of active molecules was  picked either random- or chemical diversity-based  from each target class to build a pharmacophore model  which was then used to screen the remaining compounds  in the set. Our results indicate that template sets  selected by their chemical diversity are the best  choice for similarity search tools, whereas the  optimal training sets for pharmacophore elucidators  are based on random selection underscoring that  pharmacophore modeling cannot be easily automated. We  also suggest a number of improvements for future  benchmark sets and discuss activity cliffs as a  potential problem in ligand-based virtual screening.},  issn = {1549-9596},  }  @misc{sproxel,  howpublished = {\url{http://code.google.com/p/sproxel/}},  key = {sproxel},  title = {{sproxel, r173}},  }  @article{Stierand2007,  author = {K. Stierand and M. Rarey},  journal = {ChemMedChem},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/17436259}{17436259}]  [doi:\href{http://dx.doi.org/10.1002/cmdc.200700010}{10.1002/cmdc.200700010}]},  number = {6},  pages = {853--860},  publisher = {Wiley Online Library},  title = {{From Modeling to Medicinal Chemistry: Automatic  Generation of Two{\^a}Dimensional Complex  Diagrams}},  volume = {2},  year = {2007},  issn = {1860-7187},  }  @article{Hu2005,  author = {L. Hu and M. L. Benson and R. D. Smith and  M. G. Lerner and H. A. Carlson},  journal = {Proteins: Struct Funct Bioinf},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15971202}{15971202}]  [doi:\href{http://dx.doi.org/10.1002/prot.20512}{10.1002/prot.20512}]},  number = {3},  pages = {333--340},  publisher = {Wiley Online Library},  title = {{Binding MOAD (mother of all databases)}},  volume = {60},  year = {2005},  issn = {1097-0134},  }  @article{Liu2006,  author = {T. Liu and Y. Lin and X. Wen and R. N. Jorissen and  M. K. Gilson},  journal = {Nucleic Acids Res},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/17145705}{17145705}]  [PubMed  Central:\href{http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751547}{PMC1751547}]  [doi:\href{http://dx.doi.org/10.1093/nar/gkl999}{10.1093/nar/gkl999}]},  pages = {D198},  publisher = {Oxford Univ Press},  title = {{BindingDB: a web-accessible database of  experimentally determined protein-ligand binding  affinities}},  volume = {35},  year = {2006},  issn = {0305-1048},  }  @article{Wang2005,  author = {R. Wang and X. Fang and Y. Lu and C. Y. Yang and  S. Wang},  journal = {J Med Chem},  note =  {[PubMed:\href{http://www.ncbi.nlm.nih.gov/pubmed/15943484}{15943484}]  [doi:\href{http://dx.doi.org/10.1021/jm048957q}{10.1021/jm048957q}]},  number = {12},  pages = {4111--9},  title = {{The PDBbind database: methodologies and updates}},  volume = {48},  year = {2005},  abstract = {We have developed the PDBbind database to provide a  comprehensive collection of binding affinities for  the protein-ligand complexes in the Protein Data Bank  (PDB). This paper gives a full description of the  latest version, i.e., version 2003, which is an  update to our recently reported work. Out of 23 790  entries in the PDB release No.107 (January 2004),  5897 entries were identified as protein-ligand  complexes that meet our definition. Experimentally  determined binding affinities (K(d), K(i), and  IC(50)) for 1622 of these were retrieved from the  references associated with these complexes. A total  of 900 complexes were selected to form a "refined  set", which is of particular value as a standard data  set for docking and scoring studies. All of the final  data, including binding affinity data, reference  citations, and processed structural files, have been  incorporated into the PDBbind database accessible  on-line at http:// www.pdbbind.org/.},  }