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Items: 49


D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU.

Santos-Martins D, Eberhardt J, Bianco G, Solis-Vasquez L, Ambrosio FA, Koch A, Forli S.

J Comput Aided Mol Des. 2019 Nov 6. doi: 10.1007/s10822-019-00241-9. [Epub ahead of print]


Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4.

El Khoury L, Santos-Martins D, Sasmal S, Eberhardt J, Bianco G, Ambrosio FA, Solis-Vasquez L, Koch A, Forli S, Mobley DL.

J Comput Aided Mol Des. 2019 Nov 6. doi: 10.1007/s10822-019-00240-w. [Epub ahead of print]


Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs.

Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF.

Nat Chem. 2019 Dec;11(12):1113-1123. doi: 10.1038/s41557-019-0351-5. Epub 2019 Oct 28.


SuFEx-enabled, agnostic discovery of covalent inhibitors of human neutrophil elastase.

Zheng Q, Woehl JL, Kitamura S, Santos-Martins D, Smedley CJ, Li G, Forli S, Moses JE, Wolan DW, Sharpless KB.

Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18808-18814. doi: 10.1073/pnas.1909972116. Epub 2019 Sep 4.


AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.

Zhang Y, Forli S, Omelchenko A, Sanner MF.

J Comput Chem. 2019 Dec 15;40(32):2882-2886. doi: 10.1002/jcc.26054. Epub 2019 Aug 22.


Integrative modeling of the HIV-1 ribonucleoprotein complex.

Goodsell DS, Jewett A, Olson AJ, Forli S.

PLoS Comput Biol. 2019 Jun 13;15(6):e1007150. doi: 10.1371/journal.pcbi.1007150. eCollection 2019 Jun.


Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.

Craveur P, Gres AT, Kirby KA, Liu D, Hammond JA, Deng Y, Forli S, Goodsell DS, Williamson JR, Sarafianos SG, Olson AJ.

MBio. 2019 Mar 12;10(2). pii: e02858-18. doi: 10.1128/mBio.02858-18.


AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.

Arcon JP, Modenutti CP, Avendaño D, Lopez ED, Defelipe LA, Ambrosio FA, Turjanski AG, Forli S, Marti MA.

Bioinformatics. 2019 Oct 1;35(19):3836-3838. doi: 10.1093/bioinformatics/btz152.


Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network.

Xia J, Flynn W, Gallicchio E, Uplinger K, Armstrong JD, Forli S, Olson AJ, Levy RM.

J Chem Inf Model. 2019 Apr 22;59(4):1382-1397. doi: 10.1021/acs.jcim.8b00817. Epub 2019 Feb 22.


Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone.

Mosure SA, Shang J, Eberhardt J, Brust R, Zheng J, Griffin PR, Forli S, Kojetin DJ.

J Med Chem. 2019 Feb 28;62(4):2008-2023. doi: 10.1021/acs.jmedchem.8b01573. Epub 2019 Feb 7.


Humanized GPIbα-von Willebrand factor interaction in the mouse.

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.

Blood Adv. 2018 Oct 9;2(19):2522-2532. doi: 10.1182/bloodadvances.2018023507.


Flap-site Fragment Restores Back Wild-type Behaviour in Resistant Form of HIV Protease.

Luchi A, Angelina E, Bogado L, Forli S, Olson A, Peruchena N.

Mol Inform. 2018 Dec;37(12):e1800053. doi: 10.1002/minf.201800053. Epub 2018 Jul 26.


"Inverse Drug Discovery" Strategy To Identify Proteins That Are Targeted by Latent Electrophiles As Exemplified by Aryl Fluorosulfates.

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.

J Am Chem Soc. 2018 Jan 10;140(1):200-210. doi: 10.1021/jacs.7b08366. Epub 2017 Dec 21.


Global profiling of lysine reactivity and ligandability in the human proteome.

Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF.

Nat Chem. 2017 Dec;9(12):1181-1190. doi: 10.1038/nchem.2826. Epub 2017 Jul 31.


A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain.

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.

J Biol Chem. 2016 Nov 4;291(45):23569-23577. Epub 2016 Sep 19.


Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.

Belew RK, Forli S, Goodsell DS, O'Donnell TJ, Olson AJ.

J Chem Inf Model. 2016 Aug 22;56(8):1597-607. doi: 10.1021/acs.jcim.6b00248. Epub 2016 Jul 25.


Proteome-wide covalent ligand discovery in native biological systems.

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.

Nature. 2016 Jun 23;534(7608):570-4. doi: 10.1038/nature18002. Epub 2016 Jun 15.


Natural Product Anacardic Acid from Cashew Nut Shells Stimulates Neutrophil Extracellular Trap Production and Bactericidal Activity.

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 JJ, Nizet V.

J Biol Chem. 2016 Jul 1;291(27):13964-73. doi: 10.1074/jbc.M115.695866. Epub 2016 May 13.


Directional Phosphorylation and Nuclear Transport of the Splicing Factor SRSF1 Is Regulated by an RNA Recognition Motif.

Serrano P, Aubol BE, Keshwani MM, Forli S, Ma CT, Dutta SK, Geralt M, Wüthrich K, Adams JA.

J Mol Biol. 2016 Jun 5;428(11):2430-2445. doi: 10.1016/j.jmb.2016.04.009. Epub 2016 Apr 15.


Computational protein-ligand docking and virtual drug screening with the AutoDock suite.

Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ.

Nat Protoc. 2016 May;11(5):905-19. doi: 10.1038/nprot.2016.051. Epub 2016 Apr 14.


AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.

Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF.

PLoS Comput Biol. 2015 Dec 2;11(12):e1004586. doi: 10.1371/journal.pcbi.1004586. eCollection 2015 Dec.


Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials.

Fiore M, Forli S, Manetti F.

J Med Chem. 2016 Apr 28;59(8):3609-34. doi: 10.1021/acs.jmedchem.5b01457. Epub 2015 Nov 9. Review.


Charting a Path to Success in Virtual Screening.

Forli S.

Molecules. 2015 Oct 15;20(10):18732-58. doi: 10.3390/molecules201018732. Review.


Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Bianco G, Forli S, Goodsell DS, Olson AJ.

Protein Sci. 2016 Jan;25(1):295-301. doi: 10.1002/pro.2733. Epub 2015 Jul 7.


Computational challenges of structure-based approaches applied to HIV.

Forli S, Olson AJ.

Curr Top Microbiol Immunol. 2015;389:31-51. doi: 10.1007/82_2015_432. Review.


A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.

Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ.

J Chem Inf Model. 2015 Mar 23;55(3):645-59. doi: 10.1021/ci500672v. Epub 2015 Feb 17.


Epothilones: From discovery to clinical trials.

Forli S.

Curr Top Med Chem. 2014;14(20):2312-21. Review.


Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein.

Al Olaby RR, Cocquerel L, Zemla A, Saas L, Dubuisson J, Vielmetter J, Marcotrigiano J, Khan AG, Vences Catalan F, Perryman AL, Freundlich JS, Forli S, Levy S, Balhorn R, Azzazy HM.

PLoS One. 2014 Oct 30;9(10):e111333. doi: 10.1371/journal.pone.0111333. eCollection 2014.


3D molecular models of whole HIV-1 virions generated with cellPACK.

Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ.

Faraday Discuss. 2014;169:23-44. doi: 10.1039/c4fd00017j. Epub 2014 Sep 25.


Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM.

J Phys Chem B. 2015 Jan 22;119(3):976-88. doi: 10.1021/jp506376z. Epub 2014 Sep 17.


AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.

Santos-Martins D, Forli S, Ramos MJ, Olson AJ.

J Chem Inf Model. 2014 Aug 25;54(8):2371-9. doi: 10.1021/ci500209e. Epub 2014 Jul 18.


Blind prediction of HIV integrase binding from the SAMPL4 challenge.

Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ.

J Comput Aided Mol Des. 2014 Apr;28(4):327-45. doi: 10.1007/s10822-014-9723-5. Epub 2014 Mar 5. Review.


Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM.

J Comput Aided Mol Des. 2014 Apr;28(4):475-90. doi: 10.1007/s10822-014-9711-9. Epub 2014 Feb 7.


Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

Tiefenbrunn T, Forli S, Happer M, Gonzalez A, Tsai Y, Soltis M, Elder JH, Olson AJ, Stout CD.

Chem Biol Drug Des. 2014 Feb;83(2):141-8. doi: 10.1111/cbdd.12227. Epub 2013 Oct 30.


Small molecule regulation of protein conformation by binding in the Flap of HIV protease.

Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD.

ACS Chem Biol. 2013;8(6):1223-31. doi: 10.1021/cb300611p. Epub 2013 Mar 29.


A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.

Forli S, Olson AJ.

J Med Chem. 2012 Jan 26;55(2):623-38. doi: 10.1021/jm2005145. Epub 2012 Jan 13.


Cyclin-dependent kinases 5 template: useful for virtual screening.

Pitchuanchom S, Boonyarat C, Forli S, Olson AJ, Yenjai C.

Comput Biol Med. 2012 Jan;42(1):106-11. doi: 10.1016/j.compbiomed.2011.10.014. Epub 2011 Nov 12.


N-linked peptidoresorc[4]arene-based receptors as noncompetitive inhibitors for α-chymotrypsin.

D'Acquarica I, Cerreto A, Delle Monache G, Subrizi F, Boffi A, Tafi A, Forli S, Botta B.

J Org Chem. 2011 Jun 3;76(11):4396-407. doi: 10.1021/jo102592f. Epub 2011 May 10.


Virtual Screening with AutoDock: Theory and Practice.

Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ.

Expert Opin Drug Discov. 2010 Jun 1;5(6):597-607.


A dynamic model of HIV integrase inhibition and drug resistance.

Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ.

J Mol Biol. 2010 Mar 26;397(2):600-15. doi: 10.1016/j.jmb.2010.01.033. Epub 2010 Jan 22.


Novel ester and acid derivatives of the 1,5-diarylpyrrole scaffold as anti-inflammatory and analgesic agents. Synthesis and in vitro and in vivo biological evaluation.

Biava M, Porretta GC, Poce G, Battilocchio C, Manetti F, Botta M, Forli S, Sautebin L, Rossi A, Pergola C, Ghelardini C, Galeotti N, Makovec F, Giordani A, Anzellotti P, Patrignani P, Anzini M.

J Med Chem. 2010 Jan 28;53(2):723-33. doi: 10.1021/jm901269y.


Evaluation of novel epothilone analogues by means of a common pharmacophore and a QSAR pseudoreceptor model for taxanes and epothilones.

Forli S, Manetti F, Altmann KH, Botta M.

ChemMedChem. 2010 Jan;5(1):35-40. doi: 10.1002/cmdc.200900303. No abstract available.


Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents.

Botta M, Forli S, Magnani M, Manetti F.

Top Curr Chem. 2009;286:279-328. doi: 10.1007/128_2008_20.


Synthesis, in vitro, and in vivo biological evaluation and molecular docking simulations of chiral alcohol and ether derivatives of the 1,5-diarylpyrrole scaffold as novel anti-inflammatory and analgesic agents.

Biava M, Porretta GC, Poce G, Supino S, Manetti F, Forli S, Botta M, Sautebin L, Rossi A, Pergola C, Ghelardini C, Norcini M, Makovec F, Giordani A, Anzellotti P, Cirilli R, Ferretti R, Gallinella B, La Torre F, Anzini M, Patrignani P.

Bioorg Med Chem. 2008 Sep 1;16(17):8072-81. doi: 10.1016/j.bmc.2008.07.058. Epub 2008 Jul 24.


Cyclooxygenase-2 inhibitors. 1,5-diarylpyrrol-3-acetic esters with enhanced inhibitory activity toward cyclooxygenase-2 and improved cyclooxygenase-2/cyclooxygenase-1 selectivity.

Biava M, Porretta GC, Poce G, Supino S, Forli S, Rovini M, Cappelli A, Manetti F, Botta M, Sautebin L, Rossi A, Pergola C, Ghelardini C, Vivoli E, Makovec F, Anzellotti P, Patrignani P, Anzini M.

J Med Chem. 2007 Nov 1;50(22):5403-11. Epub 2007 Oct 4.


Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems.

Forli S, Botta M.

J Chem Inf Model. 2007 Jul-Aug;47(4):1481-92. Epub 2007 Jun 22.


A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors.

Manetti F, Locatelli GA, Maga G, Schenone S, Modugno M, Forli S, Corelli F, Botta M.

J Med Chem. 2006 Jun 1;49(11):3278-86.


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