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in silico drug discovery tools


; Burkhardt, K.; Feng, Z.; Gilliland, G.L. A census of human cancer genes.

; Ferre, R.A.; Brown, E.L.; Binford, S.L. Forbes, S.A.; Beare, D.; Gunasekaran, P.; Leung, K.; Bindal, N.; Boutselakis, H.; Ding, M.; Bamford, S.; Cole, C.; Ward, S.; Kok, C.Y. Preti, D.; Baraldi, P.G. ; Dmitriev, A.V. Maggiora, G.; Vogt, M.; Stumpfe, D.; Bajorath, J. Molecular similarity in medicinal chemistry. Chenna, R.; Sugawara, H.; Koike, T.; Lopez, R.; Gibson, T.J.; Higgins, D.G. Extra precision glide, Goodsell, D.S. Salvalaglio, M.; Tiwary, P.; Parrinello, M. Assessing the reliability of the dynamics reconstructed from metadynamics. Matthews, D.A. journey that takes around 20 years from starting idea to approval and marketing of new medication.

; Sherman, W. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. To cope with this issue, a number

; Jacobson, K.A. ; Zardecki, C. The Protein Data Bank. ; Bleckman, T.M. Siegal, G.A.B. ; Gibbons, P.; Deshmukh, G.; Gustafson, A.; Kellar, T.; Lin, H.; Liu, X.; Liu, Y.; Liu, Y.; Ma, C.; Scearce-Levie, K.; Ghosh, A.S.; Shin, Y.G. How to improve R&D productivity. CLEVER, Lagorce, D.; Sperandio, O.; Galons, H.; Miteva, M.A. Challenges in modern drug discovery, Webber, S.E. Dolinsky, T.J.; Nielsen, J.E. The opportunities of mining historical and collective data in drug discovery. Grosdidier, A.; Zoete, V.; Michielin, O. SwissDock, a protein- Automated docking of flexible ligands. ; Cohen, N-C.; Rasetti, V.; Rüger, H.; Göschke, R.; Stutz, S.; Fuhrer, W.; Schilling, W.; Rigollier, P.; Yamaguchi, Y.; Cumin, F.; Baum, H-P.; Schnell, C.R. Backman, T.W.H. De Vivo, M.; Masetti, M.; Bottegoni, G.; Cavalli, A. ; Dixon, S.L. A few examples of how these tools can be problem-solving and how they may increase the success rate of a drug discovery and development program have been also provided. Virtual screening—an overview. Ratni, H.; Rogers-Evans, M.; Bissantz, C.; Grundschober, C.; Moreau, J-L.; Schuler, F.; Fischer, H.; Alvarez Sanchez, R.; Schnider, P. Discovery of highly selective brain-penetrant vasopressin 1a antagonists for the potential treatment of autism. Tarcsay, A.; Kiss, R.; Keseru, G.M.

; Morgan, P.J. ; Coleman, R.G. ; Chai, C.L.L. ; Paxton, R.J.; Black, R.A.; Bode, W. Crystal structure of the catalytic domain of human tumor necrosis factor-alpha-converting enzyme. Law, V.; Knox, C.; Djoumbou, Y.; Jewison, T.; Guo, A.C.; Liu, Y.; Maciejewski, A.; Arndt, D.; Wilson, M.; Neveu, V.; Tang, A.; Gabriel, G.; Ly, C.; Adamjee, S.; Dame, Z.T. 2015 Novel Drugs ; Welsh, W.J. ; Stratton, M.R. ; Webber, S.E. ; Jassal, B.; Jupe, S.; Matthews, L.; May, B.; Palatnik, S.; Rothfels, K.; Shamovsky, V.; Song, H.; Williams, M.; Birney, E.; Hermjakob, H.; Stein, L.; D’Eustachio, P. The Reactome pathway knowledgebase. ; Scheiber, J.; Sukuru, S.C.K. Jacobson, M.P. Hartenfeller, M.; Proschak, E.; Schüller, A.; Schneider, G. Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization. Martínez-Rosell, G.; Giorgino, T.; Harvey, M.J.; de Fabritiis, G. Drug discovery and molecular dynamics. ; Piwinski, J.J. ; Ecker, G.F.; Chichester, C. The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. Halgren, T. New method for fast and accurate binding-site identification and analysis. Shan, Y.; Kim, E.T.

van Vlijmen, H.; Desjarlais, R.L. Structure-based design of aliskiren, a novel orally effective renin inhibitor. A model for bad behavior. Web-based services for drug design and discovery. Basic local alignment search tool. Oswald, C.; Rappas, M.; Kean, J.; Doré, A.S.; Errey, J.C.; Bennett, K.; Deflorian, F.; Christopher, J.A. Schüller, A.; Hähnke, V.; Schneider, G. SmiLib v2.0. ; Krishnan, S.; Uchida, K.; Irwin, J.J.; Eidam, O.; Gibold, L.; Cimermančič, P.; Bonnet, R.; Shoichet, B.K. ; Cansfield, J.E. ; Dalal, P.; Murphy, R.B. ; Young, S.C.; Martin, H.; Mahler, J.; Brady, L.; Wilkinson, K. PRO_SELECT. Chothia, C.; Lesk, A.M. Generic GPCR residue numbers - aligning topology maps while minding the gaps.

; Frye, L.L. Chen, J.H. Vallance, P. Industry-Academic Relationship in a New Era of Drug Discovery. Gedeck, P.; Lewis, R.A. Exploiting QSAR models in lead optimization. Frey, J.G.

Bento, A.P. Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database. ; Dragovich, P.S. ; Yuen, S.T. Wang, L.; Wu, Y.; Deng, Y.; Kim, B.; Pierce, L.; Krilov, G.; Lupyan, D.; Robinson, S.; Dahlgren, M.K. Finally, selected examples where the application of in silico tools had effectively contributed to the development of marketed drugs or clinical candidates will be given. Keywords:Drug-discovery, computational chemistry, target validation, hit-to-lead, lead optimization, humangenome

A geometric approach to macromolecule-ligand interactions. ; White, H.F.; Oliver, S.W. The UniProt Consortium. Warshel, A.; Sharma, P.K. ; Mueller, U.; Skerra, A. Genheden, S.; Ryde, U. ; Green, A.R. ; Ferry, G.; Decherchi, S.; Bottegoni, G.; Ducrot, P.; Cavalli, A. Molecular dynamics simulations and kinetic measurements to estimate and predict protein-ligand residence times. ; Kato, M.; Parson, W.W. ; Springer, J.P.; Gautheron, P. Thienothiopyran-2-sulfonamides. Villoutreix, B.O. ; Saponaro, G.; Romagnoli, R.; Aghazadeh Tabrizi, M.; Baraldi, S.; Cosconati, S.; Bruno, A.; Novellino, E.; Vincenzi, F.; Ravani, A.; Borea, P.A. ChemDB update--full-text search and virtual chemical space. Gabriele Costantino, ; Holland, T.A. ; Tan, L.; Bond, P.J. Walters, W.P. ; Jacobson, K.A.

Avoiding Missed Opportunities by Analyzing the Sensitivity of Our Decisions. ; Olson, A.J. Schneider, G. Trends in virtual combinatorial library design. ; Martineau, D.; Fesik, S.W. Picas, L.; Viaud, J.; Schauer, K.; Vanni, S.; Hnia, K.; Fraisier, V.; Roux, A.; Bassereau, P.; Gaits-Iacovoni, F.; Payrastre, B.; Laporte, J.; Manneville, J-B.

Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G.L. Summary. ; DeCaprio, D. Cheminformatics approaches to analyze diversity in compound screening libraries.
Sheppard, G.S. Long-timescale molecular dynamics simulations of protein structure and function. Gasteiger, J.; Sadowski, J.; Schuur, J.; Selzer, P.; Steinhauer, L.; Steinhauer, V. Chemical Information in 3D Space. ; Luo, L.; Xia, B.; Beglov, D.; Vajda, S. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. ; Kothari, A.; Kubo, A.; Krummenacker, M.; Latendresse, M.; Mueller, L.A.; Ong, Q.; Paley, S.; Subhraveti, P.; Weaver, D.S. Discovery and optimization of anthranilic acid sulfonamides as inhibitors of methionine aminopeptidase-2, Wendt, M.D. Kawabata, T. Build-up algorithm for atomic correspondence between chemical structures.

Hussein, H.A. ; Mulholland, A. J. Computational enzymology. Icagen made a significant commitment into in silico drug discovery with its July 2016 acquisition of Sanofi’s facility in Tucson, Arizona. ; Matthews, D.A. Hsiao, Y-W.; Petersson, C.; Svensson, M.A. ; Morris, G.M. Available from: .

; Juhos, S.; Schmidtke, P.; Barril, X.; Hubbard, R.E.
Limongelli, V.; Bonomi, M.; Parrinello, M. Funnel metadynamics as accurate binding free-energy method. The weighted histogram analysis method for free-energy calculations on biomolecules. Fatty acid-binding proteins. ; Gish, W.; Miller, W.; Myers, E.W. 2014 Novel New Drugs Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain. ; Langridge, R.; Ferrin, T.E. ; Shaw, D.E. Rational design of potent sialidase-based inhibitors of influenza virus replication. ; Worland, S.T. Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. ; Zhang, H.; Nimmer, P.M.; Ng, S-C.; Shoemaker, A.R. Marco Radi* ; Mort, M.; Ball, E.V. Keywords: Drug-discovery, computational chemistry, target validation, hit-to-lead, lead optimization, humangenome Michel, J.; Tirado-Rives, J.; Jorgensen, W.L. ; Murcko, M.A. Futreal, P.A. Reymond, J-L.; Ruddigkeit, L.; Blum, L.; van Deursen, R. The Enumeration of Chemical Space. DSS.

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