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PDF of all the papers are available upon request

2020

The AutoDock Suite at 30.
Goodsell DS, Sanner M, Olson AJ, Forli S, Protein Science, 2020 Aug 17, doi:10.1002/pro.3934 (pre-print PDF)

Discovery of small-molecule enzyme activators by activity-based protein profiling.
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, Nature Chemical Biology, 2020 Sep, doi:10.1038/s41589-020-0555-4

Initial Analysis of the Arylomycin D Antibiotics.
Tan YX, Peters DS, Walsh SI, Holcomb M, Santos-Martins D, Forli S, Romesberg FE, Journal of Natural Products, 2020 Jul 24, doi:10.1021/acs.jnatprod.9b01174

An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells.
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, Cell, 2020 Aug 20, doi:10.1016/j.cell.2020.07.001

Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins.
Yan NL, Santos-Martins D, Rennella E, Sanchez BB, Chen JS, Kay LE, Wilson IA, Morgan GJ, Forli S, Kelly JW, Bioorganic & Medicinal Chemistry Letters, 2020 Aug 15, doi:10.1016/j.bmcl.2020.127356

Art and Science of the Cellular Mesoscale
David S. Goodsell, Arthur J. Olson, Stefano Forli, Trends in Biochemical Sciences 2020 Mar 21, doi:10.1021/acs.jctc.9b01248

Charting Hydrogen Bond Anisotropy.
Santos-Martins D, Forli S, Journal of Chemical Theory and Computation, 2020 Mar 10, doi:10.1021/acs.jctc.9b01248

Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity.
Xu JH, Eberhardt J, Hill-Payne B, Gonzalez-Paez GE, Castellon JO, Cravatt BF, Forli S, Wolan DW, Backus KM, ACS Chemical Biology, 2020 Feb 21, doi:10.1021/acschembio.0c00019

Structural basis for strand-transfer inhibitor binding to HIV intasomes.
Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke TR Jr, Craigie R, Lyumkis D, Science, 2020 Feb 14, doi:10.1126/science.aay8015

2019

AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.
Zhang Y, Forli S, Omelchenko A, Sanner MF, Journal of Computational Chemistry, 2019 Dec 15, doi:10.1002/jcc.26054

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, Nature Chemistry, 2019 Dec, doi:10.1038/s41557-019-0351-5

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, Journal of Computer-aided Molecular Design, 2019 Dec, doi:10.1007/s10822-019-00241-9

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, Journal of Computer-aided Molecular Design, 2019 Dec, doi:10.1007/s10822-019-00240-w

AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions.
Arcon JP, Modenutti CP, Avendano D, Lopez ED, Defelipe LA, Ambrosio FA, Turjanski AG, Forli S, Marti MA, Bioinformatics (oxford, England), 2019 Oct 1, doi:10.1093/bioinformatics/btz152

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, Proceedings of The National Academy of Sciences of The United States of America, 2019 Sep 17, doi:10.1073/pnas.1909972116

Integrative modeling of the HIV-1 ribonucleoprotein complex.
Goodsell DS, Jewett A, Olson AJ, Forli S, Plos Computational Biology, 2019 Jun, doi:10.1371/journal.pcbi.1007150

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, doi:10.1128/mBio.02858-18

Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARgamma Drug Pioglitazone.
Mosure SA, Shang J, Eberhardt J, Brust R, Zheng J, Griffin PR, Forli S, Kojetin DJ, Journal of Medicinal Chemistry, 2019 Feb 28, doi:10.1021/acs.jmedchem.8b01573

2018

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, Molecular Informatics, 2018 Dec, doi:10.1002/minf.201800053

Humanized GPIbalpha-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 Advances, 2018 Oct 9, doi:10.1182/bloodadvances.2018023507

“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, Journal of The American Chemical Society, 2018 Jan 10, doi:10.1021/jacs.7b08366

2017

Global profiling of lysine reactivity and ligandability in the human proteome.
Hacker SM, Backus KM, Lazear MR, Forli S, Correia BE, Cravatt BF, Nature Chemistry, 2017 Dec, doi:10.1038/nchem.2826

2016

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, The Journal of Biological Chemistry, 2016 Nov 4, doi:10.1074/jbc.M116.753384

Fragment-Based Analysis of Ligand Dockings Improves Classification of Actives.
Belew RK, Forli S, Goodsell DS, O’Donnell TJ, Olson AJ, Journal of Chemical Information and Modeling, 2016 Aug 22, doi:10.1021/acs.jcim.6b00248

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, The Journal of Biological Chemistry, 2016 Jul 1, doi:10.1074/jbc.M115.695866

Proteome-wide covalent ligand discovery in native biological systems.
Backus KM, Correia BE, Lum KM, Forli S, Horning BD, Gonzalez-Paez GE, Chatterjee S, Lanning BR, Teijaro JR, Olson AJ, Wolan DW, Cravatt BF, Nature, 2016 Jun 23, doi:10.1038/nature18002

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, Wuthrich K, Adams JA, Journal of Molecular Biology, 2016 Jun 5, doi:10.1016/j.jmb.2016.04.009

Computational protein-ligand docking and virtual drug screening with the AutoDock suite.
Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ, Nature Protocols, 2016 May, doi:10.1038/nprot.2016.051

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, Journal of Medicinal Chemistry, 2016 Apr 28, doi:10.1021/acs.jmedchem.5b01457

Covalent docking using autodock: Two-point attractor and flexible side chain methods.
Bianco G, Forli S, Goodsell DS, Olson AJ, Protein Science : A Publication of The Protein Society, 2016 Jan, doi:10.1002/pro.2733

2015

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.
Ravindranath PA, Forli S, Goodsell DS, Olson AJ, Sanner MF, Plos Computational Biology, 2015 Dec, doi:10.1371/journal.pcbi.1004586

Charting a Path to Success in Virtual Screening.
Forli S, Molecules (basel, Switzerland), 2015 Oct 15, doi:10.3390/molecules201018732

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, Journal of Chemical Information and Modeling, 2015 Mar 23, doi:10.1021/ci500672v

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, The Journal of Physical Chemistry. B, 2015 Jan 22, doi:10.1021/jp506376z

Computational challenges of structure-based approaches applied to HIV.
Forli S, Olson AJ, Current Topics In Microbiology and Immunology, 2015, doi:10.1007/82_2015_432

2014

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, doi:10.1371/journal.pone.0111333

3D molecular models of whole HIV-1 virions generated with cellPACK.
Johnson GT, Goodsell DS, Autin L, Forli S, Sanner MF, Olson AJ, Faraday Discussions, 2014, doi:10.1039/c4fd00017j

AutoDock4Zn: an improved AutoDock force field for small-molecule docking to zinc metalloproteins.
Santos-Martins D, Forli S, Ramos MJ, Olson AJ, Journal of Chemical Information and Modeling, 2014 Aug 25, doi:10.1021/ci500209e

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, Journal of Computer-aided Molecular Design, 2014 Apr, doi:10.1007/s10822-014-9711-9

Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein- ligand binding challenge.
Perryman AL, Santiago DN, Forli S, Martins DS, Olson AJ, Journal of Computer-aided Molecular Design, 2014 Apr, doi:10.1007/s10822-014-9709-3

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, Journal of Computer-aided Molecular Design, 2014 Apr, doi:10.1007/s10822-014-9723-5

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, Chemical Biology & Drug Design, 2014 Feb, doi:10.1111/cbdd.12227

Epothilones: From discovery to clinical trials.
Forli S, Current Topics In Medicinal Chemistry, 2014, doi:doi:10.2174/1568026614666141130095855

2013

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 Chemical Biology, 2013, doi:10.1021/cb300611p

2012

A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.
Forli S, Olson AJ, Journal of Medicinal Chemistry, 2012 Jan 26, doi:10.1021/jm2005145

Cyclin-dependent kinases 5 template: useful for virtual screening.
Pitchuanchom S, Boonyarat C, Forli S, Olson AJ, Yenjai C, Computers In Biology and Medicine, 2012 Jan, doi:10.1016/j.compbiomed.2011.10.014

2011

N-linked peptidoresorc[4]arene-based receptors as noncompetitive inhibitors for alpha-chymotrypsin.
D’Acquarica I, Cerreto A, Delle Monache G, Subrizi F, Boffi A, Tafi A, Forli S, Botta B, The Journal of Organic Chemistry, 2011 Jun 3, doi:10.1021/jo102592f

2010

Virtual Screening with AutoDock: Theory and Practice.
Cosconati S, Forli S, Perryman AL, Harris R, Goodsell DS, Olson AJ, Expert Opinion On Drug Discovery, 2010 Jun 1, doi:10.1517/17460441.2010.484460

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, Journal of Molecular Biology, 2010 Mar 26, doi:10.1016/j.jmb.2010.01.033

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, Journal of Medicinal Chemistry, 2010 Jan 28, 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, doi:10.1002/cmdc.200900303

2009

Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents.
Botta M, Forli S, Magnani M, Manetti F, Topics In Current Chemistry, 2009, doi:10.1007/128_2008_20

2008

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, Bioorganic & Medicinal Chemistry, 2008 Sep 1, doi:10.1016/j.bmc.2008.07.058

2007

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, Journal of Medicinal Chemistry, 2007 Nov 1, doi:10.1021/jm0707525

Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems.
Forli S, Botta M, Journal of Chemical Information and Modeling, 2007 Jul-Aug, doi:10.1021/ci700036j

2006

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, Journal of Medicinal Chemistry, 2006 Jun 1, doi:10.1021/jm060236z

2003

3D QSAR studies of the interaction between beta-tubulin and microtubule stabilizing antimitotic agents (MSAA). A combined pharmacophore generation and pseudoreceptor modeling approach applied to taxanes and epothilones.
Manetti F, Forli S, Maccari L, Corelli F, Botta M, Farmaco (societa Chimica Italiana : 1989), 2003 May, doi:10.1016/S0014-827X(03)00052-1