Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432:862–865

Article  CAS  PubMed  PubMed Central  Google Scholar 

Holden PM, Kaur H, Goyal R, Gochin M, Rizzo RC (2012) Footprint-based identification of viral entry inhibitors targeting HIVgp41. Bioorg Med Chem Lett 22:3011–3016

Article  CAS  PubMed  PubMed Central  Google Scholar 

Allen WJ, Rizzo RC (2012) Computer-aided approaches for targeting HIVgp41. Biology (Basel) 1:311–338

CAS  PubMed  Google Scholar 

Allen WJ, Yi HA, Gochin M, Jacobs A, Rizzo RC (2015) Small molecule inhibitors of HIVgp41 N-heptad repeat trimer formation. Bioorg Med Chem Lett 25:2853–2859

Article  CAS  PubMed  PubMed Central  Google Scholar 

McGee TD Jr, Yi HA, Allen WJ, Jacobs A, Rizzo RC (2017) Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. Bioorg Med Chem Lett 27:3177–3184

Article  CAS  PubMed  PubMed Central  Google Scholar 

Singleton CD, Humby MS, Yi HA, Rizzo RC, Jacobs A (2019) Identification of ebola virus inhibitors targeting GP2 using principles of molecular mimicry. J Virol 93:10

Article  Google Scholar 

Telehany SM, Humby MS, McGee TD Jr, Riley SP, Jacobs A, Rizzo RC (2020) Identification of Zika virus inhibitors using homology modeling and similarity-based screening to target glycoprotein E. Biochemistry 59:3709–3724

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berger WT, Ralph BP, Kaczocha M, Sun J, Balius TE, Rizzo RC, Haj-Dahmane S, Ojima I, Deutsch DG (2012) Targeting fatty acid binding protein (FABP) anandamide transporters—a novel strategy for development of anti-inflammatory and anti-nociceptive drugs. PLoS ONE 7:e50968

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kaczocha M, Rebecchi MJ, Ralph BP, Teng YH, Berger WT, Galbavy W, Elmes MW, Glaser ST, Wang L, Rizzo RC, Deutsch DG, Ojima I (2014) Inhibition of fatty acid binding proteins elevates brain anandamide levels and produces analgesia. PLoS ONE 9:e94200

Article  PubMed  PubMed Central  Google Scholar 

Hsu HC, Tong S, Zhou Y, Elmes MW, Yan S, Kaczocha M, Deutsch DG, Rizzo RC, Ojima I, Li H (2017) The antinociceptive agent SBFI-26 binds to anandamide transporters FABP5 and FABP7 at two different sites. Biochemistry 56:3454–3462

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhou Y, Elmes MW, Sweeney JM, Joseph OM, Che J, Hsu HC, Li H, Deutsch DG, Ojima I, Kaczocha M, Rizzo RC (2019) Identification of fatty acid binding protein 5 inhibitors through similarity-based screening. Biochemistry 58:4304–4316

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guo J, Collins S, Miller WT, Rizzo RC (2018) Identification of a water-coordinating HER2 inhibitor by virtual screening using similarity-based scoring. Biochemistry 57:4934–4951

Article  CAS  PubMed  PubMed Central  Google Scholar 

Collins SJ, Guo J, Rizzo RC, Miller WT (2023) Inhibition of mutationally activated HER2. Chem Biol Drug Des 101:87–102

Article  CAS  PubMed  Google Scholar 

Airola MV, Allen WJ, Pulkoski-Gross MJ, Obeid LM, Rizzo RC, Hannun YA (2015) Structural basis for ceramide recognition and hydrolysis by human neutral ceramidase. Structure 23:1482–1491

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coant N, Bickel JD, Rahaim R, Otsuka Y, Choi YM, Xu R, Simoes M, Cariello C, Mao C, Saied EM, Arenz C, Spicer TP, Bannister TD, Tonge PJ, Airola MV, Scampavia L, Hannun YA, Rizzo RC, Haley JD (2023) Neutral ceramidase-active site inhibitor chemotypes and binding modes. Bioorg Chem 139:106747

Article  CAS  PubMed  PubMed Central  Google Scholar 

Teng YH, Berger WT, Nesbitt NM, Kumar K, Balius TE, Rizzo RC, Tonge PJ, Ojima I, Swaminathan S (2015) Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotype A. Bioorg Med Chem 23:5489–5495

Article  CAS  PubMed  Google Scholar 

Zhou Y, McGillick BE, Teng YG, Haranahalli K, Ojima I, Swaminathan S, Rizzo RC (2016) Identification of small molecule inhibitors of botulinum neurotoxin serotype E via footprint similarity. Bioorg Med Chem 24:4875–4889

Article  PubMed  Google Scholar 

Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O’Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ (2019) Ultra-large library docking for discovering new chemotypes. Nature 566:224–229

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhu H, Zhang Y, Li W, Huang N (2022) A comprehensive survey of prospective structure-based virtual screening for early drug discovery in the past fifteen years. Int J Mol Sci 23:15961

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bugnon M, Röhrig UF, Goullieux M, Perez MAS, Daina A, Michielin O, Zoete VS (2024) major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024(52):W324–W332

Article  Google Scholar 

Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y (2009) Automated docking screens: a feasibility study. J Med Chem 52:5712–5720

Article  CAS  PubMed  PubMed Central  Google Scholar 

Labbé CM, Rey J, Lagorce D, Vavruša M, Becot J, Sperandio O, Villoutreix BO, Tufféry P, Miteva MA (2015) MTiOpenScreen: a web server for structure-based virtual screening. Nucleic Acids Res 43:W448-454

Article  PubMed  PubMed Central  Google Scholar 

Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking11Edited by F. E. Cohen. J Mol Biol 267:727–748

Article  CAS  PubMed  Google Scholar 

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791

Article  CAS  PubMed  PubMed Central  Google Scholar 

Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eberhardt J, Santos-Martins D, Tillack AF, Forli S (2021) AutoDock Vina 1.2.0: new docking methods, expanded force field, and python bindings. J Chem Inf Model 61:3891–3898

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK (2013) Ligand pose and orientational sampling in molecular docking. PLoS ONE 8:e75992

Article  CAS  PubMed  PubMed Central  Google Scholar 

Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC (2015) DOCK 6: impact of new features and current docking performance. J Comput Chem 36:1132–1156

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mukherjee S, Balius TE, Rizzo RC (2010) Docking validation resources: protein family and ligand flexibility experiments. J Chem Inf Model 50:1986–2000