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    title = {{'Scaffold-Hopping' by topological pharmacophore search: A contribution to virtual screening}},
    year = {1999},
    journal = {Angewandte Chemie - International Edition},
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}

@article{parks_14-benzodiazepine-25-diones_2005,
    title = {{1,4-Benzodiazepine-2,5-diones as small molecule antagonists of the {\{}HDM{\}}2–p53 interaction: discovery and {\{}SAR{\}}}},
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}

@article{wattanasin_14-diazepane-25-diones_2005,
    title = {{1,4-Diazepane-2,5-diones as novel inhibitors of {\{}LFA{\}}-1}},
    author = {Wattanasin, Sompong and Kallen, Joerg and Myers, Stewart and Guo, Qin and Sabio, Michael and Ehrhardt, Claus and Albert, Rainer and Hommel, Ulrich and Weckbecker, Gisbert and Welzenbach, Karl and Weitz-Schmidt, Gabriele},
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    volume = {15},
    doi = {10.1016/j.bmcl.2004.11.072}
}

@article{horwell_23-substituted_1997,
    title = {{2,3-Substituted 2-azanorbornanes as polar {$\beta$}-turn mimetics}},
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    volume = {7},
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}

@article{ruffoni_2-amino-3-phenylsulfanylnorbornane-2-carboxylate:_2014,
    title = {{2-Amino-3-(phenylsulfanyl)norbornane-2-carboxylate: an appealing scaffold for the design of Rac1-Tiam1 protein-protein interaction inhibitors.}},
    author = {Ruffoni, Alessandro and Ferri, Nicola and Bernini, Sergio Kevin and Ricci, Chiara and Corsini, Alberto and Maffucci, Irene and Clerici, Francesca and Contini, Alessandro},
    doi = {10.1021/jm401924s}
}

@article{mullard_2012_2013,
    title = {{2012 {\{}FDA{\}} drug approvals}},
    author = {Mullard, Asher},
    pages = {87--90},
    volume = {12},
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}

@article{clark_2d_2010,
    title = {{2D Depiction of Fragment Hierarchies}},
    author = {Clark, Alex M},
    pages = {37--46},
    volume = {50},
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}

@article{basse_2p2idb_2016,
    title = {{2P2Idb v2: Update of a structural database dedicated to orthosteric modulation of protein-protein interactions}},
    shorttitle = {2P2Idb v2},
    year = {2016},
    journal = {Database},
    author = {Basse, Marie Jeanne and Betzi, Stéphane and Morelli, Xavier and Roche, Philippe},
    volume = {2016},
    doi = {10.1093/database/baw007},
    issn = {17580463},
    pmid = {26980515},
    keywords = {Algorithms, Computational Biology, Databases, Internet, Ligands, Protein, Protein Interaction Mapping, Proteins, Software, User-Computer Interface}
}

@article{basse_2p2idb:_2013,
    title = {{2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions}},
    shorttitle = {2P2Idb},
    year = {2012},
    journal = {Nucleic Acids Research},
    author = {Basse, Marie Jeanne and Betzi, Stéphane and Bourgeas, Raphaël and Bouzidi, Sofia and Chetrit, Bernard and Hamon, Véronique and Morelli, Xavier and Roche, Philippe},
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    volume = {41},
    url = {http://nar.oxfordjournals.org/content/41/D1/D824},
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}

@article{hewings_35-dimethylisoxazoles_2011,
    title = {{3,5-dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands.}},
    author = {Hewings, David S and Wang, Minghua and Philpott, Martin and Fedorov, Oleg and Uttarkar, Sagar and Filippakopoulos, Panagis and Picaud, Sarah and Vuppusetty, Chaitanya and Marsden, Brian and Knapp, Stefan and Conway, Stuart J and Heightman, Tom D},
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    doi = {10.1021/jm200640v}
}

@article{priestle_3-d_2009,
    title = {{3-D clustering: a tool for high throughput docking}},
    author = {Priestle, John P},
    pages = {551--560},
    volume = {15},
    doi = {10.1007/s00894-008-0360-6}
}

@article{kombo_3d_2013,
    title = {{3D Molecular Descriptors Important for Clinical Success.}},
    author = {Kombo, David C and Tallapragada, Kartik and Jain, Rachit and Chewning, Joseph and Mazurov, Anatoly A and Speake, Jason D and Hauser, Terry A and Toler, Steve},
    doi = {10.1021/ci300445e}
}

@misc{novartis_ag_6-oxo.-1_2008,
    title = {{6-Oxo.-1, 6-Dihydropyrimidin-2-Yls in the Treatment of Proliferative Diseases}},
    pages = {C07D 233/ 96 A I; C07D 241/ 18 A I; C07D 403/ 10 A}
}

@article{blum_970_2009,
    title = {{970 Million druglike small molecules for virtual screening in the chemical universe database GDB-13}},
    year = {2009},
    journal = {Journal of the American Chemical Society},
    author = {Blum, Lorenz C. and Reymond, Jean Louis},
    number = {25},
    pages = {8732--8733},
    volume = {131},
    doi = {10.1021/ja902302h},
    issn = {00027863}
}

@misc{noauthor_97697_3_supp_1993189_mn3mbl.pdf_2013,
    title = {{97697{\_}3{\_}supp{\_}1993189{\_}mn3mbl.pdf - Methods}}
}

@article{ttermann_biased_2012,
    title = {{A biased ligand for {\{}OXE{\}}-R uncouples G{\&}amp;alpha; and G{\&}amp;beta;{\&}amp;gamma; signaling within a heterotrimer}},
    author = {ttermann, Stefanie Bl auml and Peters, Lucas and Ottersbach, Philipp Aaron and Bock, Andreas and Konya, Viktoria and Weaver, C David and Gonzalez, Angel and der, Ralf Schr ouml and Tyagi, Rahul and Luschnig, Petra and b, J uuml rgen G auml and Hennen, Stephanie and Ulven, Trond and Pardo, Leonardo and Mohr, Klaus and tschow, Michael G uuml and Heinemann, Akos and Kostenis, Evi},
    pages = {632--639},
    volume = {8},
    doi = {10.1038/nchembio.962}
}

@article{kraft_cell-based_nodate,
    title = {{A cell-based fascin bioassay identifies compounds with potential anti-metastasis or cognition-enhancing functions}},
    author = {Kraft, Robert and Kahn, Allon and Medina-Franco, Jose L and Orlowski, Mikayla L and Baynes, Cayla and L{\'{o}}pez-Vallejo, Fabian and Barnard, Kobus and Maggiora, Gerald M and Restifo, Linda L}
}

@article{rosania_cheminformatic_2007,
    title = {{A cheminformatic toolkit for mining biomedical knowledge}},
    year = {2007},
    journal = {Pharmaceutical Research},
    author = {Rosania, Gus R. and Crippen, Gordon and Woolf, Peter and States, David and Shedden, Kerby},
    number = {10},
    pages = {1791--1802},
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    doi = {10.1007/s11095-007-9285-5},
    issn = {07248741},
    keywords = {Bioactivity fingerprints, Bioinformatics, Chemical genetics, Chemical genomics, Chemical space, Cheminformatics, Data mining, High throughput screening, Mathematical modeling, QSAR}
}

@article{hu_comparative_2010,
    title = {{A comparative analysis of protein interfaces}},
    author = {Hu, Jing and Yan, Changhui},
    pages = {1450--1458},
    volume = {17}
}

@article{kwon_comprehensive_2012,
    title = {{A comprehensive manually curated protein-protein interaction database for the death domain superfamily}},
    year = {2012},
    journal = {Nucleic Acids Research},
    author = {Kwon, Dongseop and Yoon, Jong Hwan and Shin, Soo Yong and Jang, Tae Ho and Kim, Hong Gee and So, Insuk and Jeon, Ju Hong and Park, Hyun Ho},
    number = {D1},
    pages = {D331--6},
    volume = {40},
    doi = {10.1093/nar/gkr1149},
    issn = {03051048}
}

@article{hu_computational_2010,
    title = {{A computational analysis of the binding model of {\{}MDM{\}}2 with inhibitors}},
    author = {Hu, Guodong and Wang, Dunyou and Liu, Xinguo and Zhang, Qinggang},
    pages = {687--697},
    volume = {24},
    doi = {10.1007/s10822-010-9366-0}
}

@article{li_computer_1997,
    title = {{A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic {\{}CD{\}}4 inhibitors as novel immunotherapeutics}},
    author = {Li, S and Gao, J and Satoh, T and Friedman, T M and Edling, A E and Koch, U and Choksi, S and Han, X and Korngold, R and Huang, Z},
    pages = {73--78},
    volume = {94}
}

@article{xu_credit-card_2006,
    title = {{A credit-card library approach for disrupting protein-protein interactions}},
    author = {Xu, Y and Shi, J and Yamamoto, N and Moss, J}
}

@article{xu_credit-card_2006-1,
    title = {{A credit-card library approach for disrupting protein–protein interactions}},
    author = {Xu, Yang and Shi, Jin and Yamamoto, Noboru and Moss, Jason A and Vogt, Peter K and Janda, Kim D},
    pages = {2660--2673},
    volume = {14},
    doi = {10.1016/j.bmc.2005.11.052}
}

@article{bucci_decade_2010,
    title = {{A decade of chemical biology}},
    author = {Bucci, M and Goodman, C}
}

@article{hajduk_decade_2007,
    title = {{A decade of fragment-based drug design: strategic advances and lessons learned}},
    author = {Hajduk, Philip J and Greer, Jonathan},
    pages = {211--219},
    volume = {6},
    doi = {10.1038/nrd2220}
}

@article{godden_distance_2006,
    title = {{A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations}},
    author = {Godden, Jeffrey W and Bajorath, Jürgen},
    pages = {1094--1097},
    volume = {46},
    doi = {10.1021/ci050510i}
}

@article{arnaud_dominant_2010,
    title = {{A dominant mutation in the gene encoding the erythroid transcription factor {\{}KLF{\}}1 causes a congenital dyserythropoietic anemia}},
    author = {Arnaud, Lionel and Saison, Carole and Helias, Virginie and Lucien, Nicole and Steschenko, Dominique and Giarratana, Marie-Catherine and Prehu, Claude and Foliguet, Bernard and Montout, Lory and de Brevern, Alexandre G and Francina, Alain and Ripoche, Pierre and Fenneteau, Odile and Da Costa, Lydie and Peyrard, Thierry and Coghlan, Gail and Illum, Niels and Birgens, Henrik and Tamary, Hannah and Iolascon, Achille and Delaunay, Jean and Tchernia, Gil and Cartron, Jean-Pierre},
    number = {5},
    pages = {721--727},
    volume = {87},
    doi = {10.1016/j.ajhg.2010.10.010},
    issn = {1537-6605},
    pmid = {21055716},
    keywords = {Anemia, Base Sequence, Cell Differentiation, Congenital, Dyserythropoietic, Erythroblasts, Erythropoiesis, Humans, Infant, Kruppel-Like Transcription Factors, Male, Models, Molecular, Mutation, Newborn}
}

@article{ouizougun-oubari_druggable_2015,
    title = {{A Druggable Pocket at the Nucleocapsid/Phosphoprotein Interaction Site of Human Respiratory Syncytial Virus}},
    year = {2015},
    journal = {Journal of Virology},
    author = {Ouizougun-Oubari, Mohamed and Pereira, Nelson and Tarus, Bogdan and Galloux, Marie and Lassoued, Safa and Fix, Jenna and Tortorici, M. Alejandra and Hoos, Sylviane and Baron, Bruno and England, Patrick and Desma{\"{e}}le, Didier and Couvreur, Patrick and Bontems, François and Rey, Félix A. and El{\'{e}}ou{\"{e}}t, Jean-François and Sizun, Christina and Slama-Schwok, Anny and Duquerroy, Stéphane},
    number = {21},
    pages = {11129--11143},
    volume = {89},
    doi = {10.1128/jvi.01612-15},
    issn = {0022-538X},
    pmid = {26246564},
    keywords = {Antiviral Agents, Calorimetry, Crystallography, Drug Design, Human, Humans, Luminescent Proteins, Magnetic Resonance Spectroscopy, Models, Molecular, Nucleocapsid, Phosphoproteins, Protein Conformation, Respiratory Syncytial Virus, Respiratory Syncytial Virus Infections, X-Ray, X-Ray Diffraction}
}

@article{caporuscio_dynamic_2009,
    title = {{A dynamic target-based pharmacophoric model mapping the CD4 binding site on HIV-1 gp120 to identify new inhibitors of gp120-CD4 protein-protein interactions}},
    year = {2009},
    journal = {Bioorganic and Medicinal Chemistry Letters},
    author = {Caporuscio, Fabiana and Tafi, Andrea and Gonz{\'{a}}lez, Emmanuel and Manetti, Fabrizio and Est{\'{e}}, José A. and Botta, Maurizio},
    number = {21},
    pages = {6087--6091},
    volume = {19},
    doi = {10.1016/j.bmcl.2009.09.029},
    issn = {0960894X},
    keywords = {Pharmacophore modeling, Phe43 cavity, Protein-protein interactions, Structure-based drug design, gp120-CD4 interactions}
}

@article{caporuscio_dynamic_2009-1,
    title = {{A dynamic target-based pharmacophoric model mapping the {\{}CD{\}}4 binding site on {\{}HIV{\}}-1 gp120 to identify new inhibitors of gp120-{\{}CD{\}}4 protein-protein interactions}},
    author = {Caporuscio, Fabiana and Tafi, Andrea and Gonz{\'{a}}lez, Emmanuel and Manetti, Fabrizio and Est{\'{e}}, José A and Botta, Maurizio},
    pages = {6087--6091},
    volume = {19},
    doi = {10.1016/j.bmcl.2009.09.029}
}

@article{cho_feature-based_2009,
    title = {{A feature-based approach to modeling protein-protein interaction hot spots}},
    author = {Cho, Kyu-il and Kim, Dongsup and Lee, Doheon},
    pages = {2672--2687},
    volume = {37},
    doi = {10.1093/nar/gkp132}
}

@article{tsuganezawa_fluorescent-based_2013,
    title = {{A fluorescent-based high-throughput screening assay for small molecules that inhibit the interaction of MdmX with p53}},
    year = {2013},
    journal = {Journal of Biomolecular Screening},
    author = {Tsuganezawa, Keiko and Nakagawa, Yukari and Kato, Miki and Taruya, Shigenao and Takahashi, Fumio and Endoh, Morio and Utata, Rei and Mori, Masumi and Ogawa, Naoko and Honma, Teruki and Yokoyama, Shigeyuki and Hashizume, Yoshinobu and Aoki, Masaaki and Kasai, Takuma and Kigawa, Takanori and Kojima, Hirotatsu and Okabe, Takayoshi and Nagano, Tetsuo and Tanaka, Akiko},
    number = {2},
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    volume = {18},
    doi = {10.1177/1087057112460729},
    issn = {10870571},
    keywords = {Mdm2, MdmX, fluorescence, p53, protein-protein interaction}
}

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}

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@article{gustafsson_case_2004,
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    journal = {Nature Reviews Drug Discovery},
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@article{chen_novel_2012,
    title = {{A novel obatoclax derivative, {\{}SC{\}}-2001, induces apoptosis in hepatocellular carcinoma cells through {\{}SHP{\}}-1-dependent {\{}STAT{\}}3 inactivation.}},
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@article{chahil_novel_2012,
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@article{zinzalla_novel_2010,
    title = {{A novel small-molecule inhibitor of IL-6 signalling}},
    year = {2010},
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    doi = {10.1016/j.bmcl.2010.09.117},
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    keywords = {IL-6 signalling, Inhibitor, STAT3, Small molecule}
}

@article{yan_novel_2010,
    title = {{A Novel Water-Soluble Gossypol Derivative Increases Chemotherapeutic Sensitivity and Promotes Growth Inhibition in Colon Cancer}},
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@article{schimmer_phase_2008,
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@article{singh_physicochemical_2012,
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@article{cai_potent_2011,
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@article{olbe_proton-pump_2003,
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@article{knapp_public-private_2012,
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@article{frank_ratchet-like_2000,
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    keywords = {Biological Transport, Cryoelectron Microscopy, Escherichia coli, Guanosine Triphosphate/metabolism, Hydrolysis, Macromolecular Substances, Messenger/metabolism, Models, Molecular, Molecular Conformation, Peptide Elongation Factor G/metabolism, Ribosomes/chemistry/metabolism/*ultrastructure, Transfer/metabolism, {\{}RNA{\}}}
}

@article{wetzel_scaffold-tree-merging_2010,
    title = {{A scaffold-tree-merging strategy for prospective bioactivity annotation of gamma-pyrones}},
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}

@article{deursen_searchable_2010,
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@article{anders_semisynthetic_2013,
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    author = {Anders, Carolin and Higuchi, Yusuke and Koschinsky, Kristin and Bartel, Maria and Schumacher, Benjamin and Thiel, Philipp and Nitta, Hajime and Preisig-M{\"{u}}ller, Regina and Schlichth{\"{o}}rl, Günter and Renigunta, Vijay and Ohkanda, Junko and Daut, Jürgen and Kato, Nobuo and Ottmann, Christian},
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    volume = {20},
    doi = {10.1016/j.chembiol.2013.03.015},
    issn = {1879-1301},
    pmid = {23601647},
    keywords = {14-3-3 Proteins, Amino Acid Sequence, Animals, Binding Sites, Biological Transport, Cell Membrane, Crystallography, Diterpenes, Humans, Kinetics, Molecular Conformation, Molecular Sequence Data, Oocytes, Potassium Channels, Protein Binding, Protein Interaction Domains and Motifs, Protein Stability, Protein Structure, Tandem Pore Domain, Tertiary, X-Ray, Xenopus laevis}
}

@article{rush_shape-based_2005,
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@article{erkizan_small_2009,
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@article{zhou_small_2013,
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@article{cerchietti_small-molecule_2010,
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@article{tuncbag_survey_2009,
    title = {{A survey of available tools and web servers for analysis of protein–protein interactions and interfaces}},
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    pages = {1143--1152},
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    doi = {10.1016/j.chembiol.2011.06.013},
    keywords = {new target, {\{}PPI{\}}}
}

@article{ekins_turning_2009,
    title = {{A Turning Point For Blood–Brain Barrier Modeling}},
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    pages = {3461--3471},
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    doi = {10.1021/ja038855+}
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@article{tse_abt-263:_2008,
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@article{kim_accelerated_2012,
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@article{kamisetty_accounting_2011,
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@article{yecies_acquired_2010,
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    pages = {3304--3313},
    volume = {115},
    doi = {10.1182/blood-2009-07-233304},
    issn = {1528-0020 (Electronic) 0006-4971 (Linking)},
    keywords = {Antineoplastic Agents/*pharmacology, Apoptosis Regulatory Proteins/metabolism, Biphenyl Compounds/*pharmacology, Cell Line, Diffuse/genetics/*metabolism, Drug Resistance, Gene Expression, Gene Expression Profiling, Humans, Immunoblotting, Immunoprecipitation, Large B-Cell, Lymphoma, Membrane Proteins/metabolism, Myeloid Cell Leukemia Sequence 1 Protein, Neoplasm/*genetics, Nitrophenols/*pharmacology, Piperazines/pharmacology, Proto-Oncogene Proteins c-bcl-2/genetics/*metabol, Proto-Oncogene Proteins/metabolism, Reverse Transcriptase Polymerase Chain Reaction, Sulfonamides/*pharmacology, Tumor, Up-Regulation, {\{}BH{\}}3 Interacting Domain Death Agonist Protein/me}
}

@article{graves_activation_2012,
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@article{tang_acylpyrogallols_2008,
    title = {{Acylpyrogallols as Inhibitors of Antiapoptotic Bcl-2 Proteins}},
    author = {Tang, Guozhi and Nikolovska-Coleska, Zaneta and Qiu, Su and Yang, Chao-Yie and Guo, Jie and Wang, Shaomeng},
    pages = {717--720},
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    journal = {Angewandte Chemie - International Edition},
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    pages = {7111--7115},
    volume = {49},
    doi = {10.1002/anie.201001739},
    issn = {14337851},
    keywords = {Conformational analysis, Molecular modeling, Peptide mimics, Protein-protein interactions, Ring-closing metathesis}
}

@article{de_bodinat_agomelatine_2010,
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@article{wang_amino-substituted_2005,
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@article{waring_analysis_2015,
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    pages = {475--486},
    volume = {14},
    doi = {10.1038/nrd4609},
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    keywords = {Animals, Drug Delivery Systems, Drug Discovery, Drug Evaluation, Drug Industry, Drugs, Humans, Investigational, Preclinical, Statistics as Topic}
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@article{perola_analysis_2010,
    title = {{An analysis of the binding efficiencies of drugs and their leads in successful drug discovery programs}},
    author = {Perola, Emanuele},
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@article{xue_effective_2013,
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    author = {Xue, Xin and Sun, Haopeng},
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@article{venkatesan_empirical_2008,
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    author = {Venkatesan, Kavitha and Rual, Jean-François and Vazquez, Alexei and Stelzl, Ulrich and Lemmens, Irma and Hirozane-Kishikawa, Tomoko and Hao, Tong and Zenkner, Martina and Xin, Xiaofeng and Goh, Kwang-Il and Yildirim, Muhammed A and Simonis, Nicolas and Heinzmann, Kathrin and Gebreab, Fana and Sahalie, Julie M and Cevik, Sebiha and Simon, Christophe and de Smet, Anne-Sophie and Dann, Elizabeth and Smolyar, Alex and Vinayagam, Arunachalam and Yu, Haiyuan and Szeto, David and Borick, Heather and Dricot, Amélie and Klitgord, Niels and Murray, Ryan R and Lin, Chenwei and Lalowski, Maciej and Timm, Jan and Rau, Kirstin and Boone, Charles and Braun, Pascal and Cusick, Michael E and Roth, Frederick P and Hill, David E and Tavernier, Jan and Wanker, Erich E and Barab{\'{a}}si, Albert-László and Vidal, Marc},
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@article{oltersdorf_inhibitor_2005,
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@article{bourgeas_atomic_2010-1,
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@article{vogt_bayesian_2007,
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