My Bibliography

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Bianco G, Holcomb M, Santos-Martins D, Tillack A, Hansel-Harris A, Forli S. Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species. J Chem Inf Model. 2023 Sep 11;63(17):5631-5640. doi: 10.1021/acs.jcim.3c00832. Epub 2023 Aug 28. PubMed PMID: 37639635.

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Eberhardt J, Forli S. WaterKit: Thermodynamic Profiling of Protein Hydration Sites. J Chem Theory Comput. 2023 May 9;19(9):2535-2556. doi: 10.1021/acs.jctc.2c01087. Epub 2023 Apr 24. PubMed PMID: 37094087.

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Adams ZC, Silvestri AP, Chiorean S, Flood DT, Balo BP, Shi Y, Holcomb M, Walsh SI, Maillie CA, Pierens GK, Forli S, Rosengren KJ, Dawson PE. Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS Cent Sci. 2023 Apr 26;9(4):648-656. doi: 10.1021/acscentsci.2c01462. eCollection 2023 Apr 26. PubMed PMID: 37122474; PubMed Central PMCID: PMC10141592.

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Hansel-Harris AT, Santos-Martins D, Bruciaferri N, Tillack AF, Holcomb M, Forli S. Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results. J Chem Inf Model. 2023 Apr 10;63(7):1858-1864. doi: 10.1021/acs.jcim.3c00166. Epub 2023 Mar 28. PubMed PMID: 36976961; NIHMSID:NIHMS1947070.

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Laboute T, Zucca S, Holcomb M, Patil DN, Garza C, Wheatley BA, Roy RN, Forli S, Martemyanov KA. Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR. Science. 2023 Mar 31;379(6639):1352-1358. doi: 10.1126/science.add7150. Epub 2023 Mar 30. PubMed PMID: 36996198.

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Holcomb M, Chang YT, Goodsell DS, Forli S. Evaluation of AlphaFold2 structures as docking targets. Protein Sci. 2023 Jan;32(1):e4530. doi: 10.1002/pro.4530. PubMed PMID: 36479776; PubMed Central PMCID: PMC9794023.

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Cheng Y, Li G, Smedley CJ, Giel MC, Kitamura S, Woehl JL, Bianco G, Forli S, Homer JA, Cappiello JR, Wolan DW, Moses JE, Sharpless KB. Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2208540119. doi: 10.1073/pnas.2208540119. Epub 2022 Sep 7. PubMed PMID: 36070343; PubMed Central PMCID: PMC9478681.

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Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R. Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J Comput Aided Mol Des. 2022 Mar;36(3):193-203. doi: 10.1007/s10822-022-00446-5. Epub 2022 Mar 9. PubMed PMID: 35262811; PubMed Central PMCID: PMC8904208.

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Solis-Vasquez L, Tillack AF, Santos-Martins D, Koch A, LeGrand S, Forli S. Benchmarking the Performance of Irregular Computations in AutoDock-GPU Molecular Docking. Parallel Comput. 2022 Mar;109. doi: 10.1016/j.parco.2021.102861. Epub 2021 Nov 11. PubMed PMID: 34898769; PubMed Central PMCID: PMC8654209.

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Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J Chem Inf Model. 2021 Aug 23;61(8):3891-3898. doi: 10.1021/acs.jcim.1c00203. Epub 2021 Jul 19. PubMed PMID: 34278794; PubMed Central PMCID: PMC10683950.

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Sanner MF, Dieguez L, Forli S, Lis E. Improving Docking Power for Short Peptides Using Random Forest. J Chem Inf Model. 2021 Jun 28;61(6):3074-3090. doi: 10.1021/acs.jcim.1c00573. Epub 2021 Jun 14. PubMed PMID: 34124893; PubMed Central PMCID: PMC8543977.

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Yan NL, Santos-Martins D, Nair R, Chu A, Wilson IA, Johnson KA, Forli S, Morgan GJ, Petrassi HM, Kelly JW. Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. J Med Chem. 2021 May 13;64(9):6273-6299. doi: 10.1021/acs.jmedchem.1c00339. Epub 2021 May 3. PubMed PMID: 33939422; PubMed Central PMCID: PMC8428256.

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Santos-Martins D, Solis-Vasquez L, Tillack AF, Sanner MF, Koch A, Forli S. Accelerating AutoDock4 with GPUs and Gradient-Based Local Search. J Chem Theory Comput. 2021 Feb 9;17(2):1060-1073. doi: 10.1021/acs.jctc.0c01006. Epub 2021 Jan 6. PubMed PMID: 33403848; PubMed Central PMCID: PMC8063785.

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Arcon JP, Turjanski AG, Martí MA, Forli S. Biased Docking for Protein-Ligand Pose Prediction. Methods Mol Biol. 2021;2266:39-72. doi: 10.1007/978-1-0716-1209-5_3. PubMed PMID: 33759120; NIHMSID:NIHMS1947069.

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Goodsell DS, Sanner MF, Olson AJ, Forli S. The AutoDock suite at 30. Protein Sci. 2021 Jan;30(1):31-43. doi: 10.1002/pro.3934. Epub 2020 Sep 12. PubMed PMID: 32808340; PubMed Central PMCID: PMC7737764.

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Acharya A, Agarwal R, Baker MB, Baudry J, Bhowmik D, Boehm S, Byler KG, Chen SY, Coates L, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glaser J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller DW, Kovalevsky A, Larkin J, Lawrence TJ, LeGrand S, Liu SH, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Poole D, Pouchard L, Ramanathan A, Rogers DM, Santos-Martins D, Scheinberg A, Sedova A, Shen Y, Smith JC, Smith MD, Soto C, Tsaris A, Thavappiragasam M, Tillack AF, Vermaas JV, Vuong VQ, Yin J, Yoo S, Zahran M, Zanetti-Polzi L. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J Chem Inf Model. 2020 Dec 28;60(12):5832-5852. doi: 10.1021/acs.jcim.0c01010. Epub 2020 Dec 16. PubMed PMID: 33326239; PubMed Central PMCID: PMC7754786.

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Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat Struct Mol Biol. 2020 Dec;27(12):1194-1201. doi: 10.1038/s41594-020-00520-2. Epub 2020 Oct 26. PubMed PMID: 33106659; PubMed Central PMCID: PMC7718406.

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Bianco G, Goodsell DS, Forli S. Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors. Trends Pharmacol Sci. 2020 Dec;41(12):1038-1049. doi: 10.1016/j.tips.2020.10.005. Epub 2020 Nov 2. Review. PubMed PMID: 33153778; PubMed Central PMCID: PMC7669701.

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Ozorowski G, Torres JL, Santos-Martins D, Forli S, Ward AB. A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Cell Rep. 2020 Nov 24;33(8):108428. doi: 10.1016/j.celrep.2020.108428. PubMed PMID: 33238117; PubMed Central PMCID: PMC7701285.

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Kok BP, Ghimire S, Kim W, Chatterjee S, Johns T, Kitamura S, Eberhardt J, Ogasawara D, Xu J, Sukiasyan A, Kim SM, Godio C, Bittencourt JM, Cameron M, Galmozzi A, Forli S, Wolan DW, Cravatt BF, Boger DL, Saez E. Discovery of small-molecule enzyme activators by activity-based protein profiling. Nat Chem Biol. 2020 Sep;16(9):997-1005. doi: 10.1038/s41589-020-0555-4. Epub 2020 Jun 8. PubMed PMID: 32514184; PubMed Central PMCID: PMC7442688.

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Vinogradova EV, Zhang X, Remillard D, Lazar DC, Suciu RM, Wang Y, Bianco G, Yamashita Y, Crowley VM, Schafroth MA, Yokoyama M, Konrad DB, Lum KM, Simon GM, Kemper EK, Lazear MR, Yin S, Blewett MM, Dix MM, Nguyen N, Shokhirev MN, Chin EN, Lairson LL, Melillo B, Schreiber SL, Forli S, Teijaro JR, Cravatt BF. An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. Cell. 2020 Aug 20;182(4):1009-1026.e29. doi: 10.1016/j.cell.2020.07.001. Epub 2020 Jul 29. PubMed PMID: 32730809; PubMed Central PMCID: PMC7775622.

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Yan NL, Santos-Martins D, Rennella E, Sanchez BB, Chen JS, Kay LE, Wilson IA, Morgan GJ, Forli S, Kelly JW. Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins. Bioorg Med Chem Lett. 2020 Aug 15;30(16):127356. doi: 10.1016/j.bmcl.2020.127356. Epub 2020 Jun 16. PubMed PMID: 32631553; PubMed Central PMCID: PMC7402200.

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Tan YX, Peters DS, Walsh SI, Holcomb M, Santos-Martins D, Forli S, Romesberg FE. Initial Analysis of the Arylomycin D Antibiotics. J Nat Prod. 2020 Jul 24;83(7):2112-2121. doi: 10.1021/acs.jnatprod.9b01174. Epub 2020 Jul 2. PubMed PMID: 32614583.

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Goodsell DS, Olson AJ, Forli S. Art and Science of the Cellular Mesoscale. Trends Biochem Sci. 2020 Jun;45(6):472-483. doi: 10.1016/j.tibs.2020.02.010. Epub 2020 Mar 21. Review. PubMed PMID: 32413324; PubMed Central PMCID: PMC7230070.

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Santos-Martins D, Forli S. Charting Hydrogen Bond Anisotropy. J Chem Theory Comput. 2020 Apr 14;16(4):2846-2856. doi: 10.1021/acs.jctc.9b01248. Epub 2020 Mar 10. PubMed PMID: 32105473; PubMed Central PMCID: PMC7325729.

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Xu JH, Eberhardt J, Hill-Payne B, González-Páez GE, Castellón JO, Cravatt BF, Forli S, Wolan DW, Backus KM. Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity. ACS Chem Biol. 2020 Feb 21;15(2):575-586. doi: 10.1021/acschembio.0c00019. Epub 2020 Jan 23. PubMed PMID: 31927936; PubMed Central PMCID: PMC7370820.

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Passos DO, Li M, Jóźwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke TR Jr, Craigie R, Lyumkis D. Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science. 2020 Feb 14;367(6479):810-814. doi: 10.1126/science.aay8015. Epub 2020 Jan 30. PubMed PMID: 32001521; PubMed Central PMCID: PMC7357238.

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Zhang Y, Forli S, Omelchenko A, Sanner MF. AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools. J Comput Chem. 2019 Dec 15;40(32):2882-2886. doi: 10.1002/jcc.26054. Epub 2019 Aug 22. PubMed PMID: 31436329; PubMed Central PMCID: PMC7737998.

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Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF. Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs. Nat Chem. 2019 Dec;11(12):1113-1123. doi: 10.1038/s41557-019-0351-5. Epub 2019 Oct 28. PubMed PMID: 31659311; PubMed Central PMCID: PMC6874898.

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Santos-Martins D, Eberhardt J, Bianco G, Solis-Vasquez L, Ambrosio FA, Koch A, Forli S. D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU. J Comput Aided Mol Des. 2019 Dec;33(12):1071-1081. doi: 10.1007/s10822-019-00241-9. Epub 2019 Nov 6. PubMed PMID: 31691920; PubMed Central PMCID: PMC7325737.

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El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL. Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4. J Comput Aided Mol Des. 2019 Dec;33(12):1011-1020. doi: 10.1007/s10822-019-00240-w. Epub 2019 Nov 6. PubMed PMID: 31691919; PubMed Central PMCID: PMC7027993.

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Arcon JP, Modenutti CP, Avendaño D, Lopez ED, Defelipe LA, Ambrosio FA, Turjanski AG, Forli S, Marti MA. AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions. Bioinformatics. 2019 Oct 1;35(19):3836-3838. doi: 10.1093/bioinformatics/btz152. PubMed PMID: 30825370; PubMed Central PMCID: PMC6761960.

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Zheng Q, Woehl JL, Kitamura S, Santos-Martins D, Smedley CJ, Li G, Forli S, Moses JE, Wolan DW, Sharpless KB. SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase. Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18808-18814. doi: 10.1073/pnas.1909972116. Epub 2019 Sep 4. PubMed PMID: 31484779; PubMed Central PMCID: PMC6754619.

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Goodsell DS, Jewett A, Olson AJ, Forli S. Integrative modeling of the HIV-1 ribonucleoprotein complex. PLoS Comput Biol. 2019 Jun;15(6):e1007150. doi: 10.1371/journal.pcbi.1007150. eCollection 2019 Jun. PubMed PMID: 31194731; PubMed Central PMCID: PMC6592547.

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Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM. Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. J Chem Inf Model. 2019 Apr 22;59(4):1382-1397. doi: 10.1021/acs.jcim.8b00817. Epub 2019 Feb 22. PubMed PMID: 30758197; PubMed Central PMCID: PMC6496938.

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Craveur P, Gres AT, Kirby KA, Liu D, Hammond JA, Deng Y, Forli S, Goodsell DS, Williamson JR, Sarafianos SG, Olson AJ. Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket. mBio. 2019 Mar 12;10(2). doi: 10.1128/mBio.02858-18. PubMed PMID: 30862755; PubMed Central PMCID: PMC6414707.

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Mosure SA, Shang J, Eberhardt J, Brust R, Zheng J, Griffin PR, Forli S, Kojetin DJ. Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone. J Med Chem. 2019 Feb 28;62(4):2008-2023. doi: 10.1021/acs.jmedchem.8b01573. Epub 2019 Feb 7. PubMed PMID: 30676741; PubMed Central PMCID: PMC6898968.

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Luchi A, Angelina E, Bogado L, Forli S, Olson A, Peruchena N. Flap-site Fragment Restores Back Wild-type Behaviour in Resistant Form of HIV Protease. Mol Inform. 2018 Dec;37(12):e1800053. doi: 10.1002/minf.201800053. Epub 2018 Jul 26. PubMed PMID: 30051611; PubMed Central PMCID: PMC6501176.

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Kanaji S, Orje JN, Kanaji T, Kamikubo Y, Morodomi Y, Chen Y, Zarpellon A, Eberhardt J, Forli S, Fahs SA, Sood R, Haberichter SL, Montgomery RR, Ruggeri ZM. Humanized GPIbα-von Willebrand factor interaction in the mouse. Blood Adv. 2018 Oct 9;2(19):2522-2532. doi: 10.1182/bloodadvances.2018023507. PubMed PMID: 30287479; PubMed Central PMCID: PMC6177644.

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Mortenson DE, Brighty GJ, Plate L, Bare G, Chen W, Li S, Wang H, Cravatt BF, Forli S, Powers ET, Sharpless KB, Wilson IA, Kelly JW. "Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates. J Am Chem Soc. 2018 Jan 10;140(1):200-210. doi: 10.1021/jacs.7b08366. Epub 2017 Dec 21. PubMed PMID: 29265822; PubMed Central PMCID: PMC5762408.

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Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF. Global profiling of lysine reactivity and ligandability in the human proteome. Nat Chem. 2017 Dec;9(12):1181-1190. doi: 10.1038/nchem.2826. Epub 2017 Jul 31. PubMed PMID: 29168484; PubMed Central PMCID: PMC5726523.

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Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. J Biol Chem. 2016 Nov 4;291(45):23569-23577. doi: 10.1074/jbc.M116.753384. Epub 2016 Sep 19. PubMed PMID: 27645997; PubMed Central PMCID: PMC5095411.

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Belew RK, Forli S, Goodsell DS, O'Donnell TJ, Olson AJ. Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives. J Chem Inf Model. 2016 Aug 22;56(8):1597-607. doi: 10.1021/acs.jcim.6b00248. Epub 2016 Jul 25. PubMed PMID: 27384036; PubMed Central PMCID: PMC5023760.

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Hollands A, Corriden R, Gysler G, Dahesh S, Olson J, Raza Ali S, Kunkel MT, Lin AE, Forli S, Newton AC, Kumar GB, Nair BG, Perry JJP, Nizet V. Natural Product Anacardic Acid from Cashew Nut Shells Stimulates Neutrophil Extracellular Trap Production and Bactericidal Activity. J Biol Chem. 2016 Jul 1;291(27):13964-13973. doi: 10.1074/jbc.M115.695866. Epub 2016 May 13. PubMed PMID: 27226531; PubMed Central PMCID: PMC4933157.

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Backus KM, Correia BE, Lum KM, Forli S, Horning BD, González-Páez GE, Chatterjee S, Lanning BR, Teijaro JR, Olson AJ, Wolan DW, Cravatt BF. Proteome-wide covalent ligand discovery in native biological systems. Nature. 2016 Jun 23;534(7608):570-4. doi: 10.1038/nature18002. Epub 2016 Jun 15. PubMed PMID: 27309814; PubMed Central PMCID: PMC4919207.

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Serrano P, Aubol BE, Keshwani MM, Forli S, Ma CT, Dutta SK, Geralt M, Wüthrich K, Adams JA. Directional Phosphorylation and Nuclear Transport of the Splicing Factor SRSF1 Is Regulated by an RNA Recognition Motif. J Mol Biol. 2016 Jun 5;428(11):2430-2445. doi: 10.1016/j.jmb.2016.04.009. Epub 2016 Apr 15. PubMed PMID: 27091468; PubMed Central PMCID: PMC4884534.

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Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc. 2016 May;11(5):905-19. doi: 10.1038/nprot.2016.051. Epub 2016 Apr 14. PubMed PMID: 27077332; PubMed Central PMCID: PMC4868550.

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Fiore M, Forli S, Manetti F. Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials. J Med Chem. 2016 Apr 28;59(8):3609-34. doi: 10.1021/acs.jmedchem.5b01457. Epub 2015 Nov 9. Review. PubMed PMID: 26502061; PubMed Central PMCID: PMC4850115.

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Bianco G, Forli S, Goodsell DS, Olson AJ. Covalent docking using autodock: Two-point attractor and flexible side chain methods. Protein Sci. 2016 Jan;25(1):295-301. doi: 10.1002/pro.2733. Epub 2015 Jul 7. PubMed PMID: 26103917; PubMed Central PMCID: PMC4815316.

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Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility. PLoS Comput Biol. 2015 Dec;11(12):e1004586. doi: 10.1371/journal.pcbi.1004586. eCollection 2015 Dec. PubMed PMID: 26629955; PubMed Central PMCID: PMC4667975.