2024
Assessing AF2’s ability to predict structural ensembles of proteins
Riccabona JR, Spoendlin FC, Fischer ALM, Loeffler JR, Quoika PK, Jenkins TP, Ferguson JA, Smorodina E, Laustsen AH, Greiff V, Forli S, Ward AB, Deane CM, Fernández-Quintero ML
Structure, 2024
The role of force fields and water models in protein folding and unfolding dynamics
Fischer ALM, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibi F, Quoika PK, Gshwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML
Journal of Chemical Theory and Computation, 2024
Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms
Huynh H, Le K, Vu L, Nguyen T, Holcomb M, Forli S, Phan H
Journal of Computational Chemistry, 2024
Enhanced mapping of small molecule binding sites in cells
Wozniak JM; Li W, Governa P, Chen LY, Jadhav AJ, Dongre A, Forli S, Parker CG
Nature Chem Biol, 2024
Consensus screening for a challenging target: The quest for P-glycoprotein inhibitors
Governa P, Biagi M, Manetti F, Forli S
RSC Medicinal Chemistry, 2024
2023
Reactive docking: A computational method for high-throughput virtual screenings of reactive species
Bianco G, Holcomb M, Santos-Martins D, Hansel-Harris A, Forli S
ChemRxiv, 2023
Richard Lerner’s bioinspiration: Biomolecular visualization and modeling at Scripps Research
Olson AJ, Sanner MF, Goodsell DS, Forli S
Israel Journal of Chemistry, 2023
Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR
Laboute T, Zucca S, Holcomb M, Patil DN, Garza C, Wheatley BA, Roy RN, Forli S, Martemyanov KA
Science, 2023
WaterKit: Thermodynamic profiling of protein hydration sites
Eberhardt J, Forli S
Journal of Chemical Theory and Computation, 2023
Ringtail: A Python tool for efficient management and storage of virtual screening results
Hansel-Harris A, Santos-Martins D, Bruciaferri N, Tillack AF, Holcomb M, Forli S
Journal of Chemical Information and Modeling, 2023
Stretching peptides to generate small molecule β-strand mimics
Adams Z, Silvestri A, Chiorean S, Flood D, Balo B, Shi Y, Holcomb M, Walsh S, Maillie C, Pierens G, Forli S, Rosengren K, Dawson P
ACS Central Science, 2023
Evaluation of AlphaFold2 structures as docking targets
Holcomb M, Chang Y-T, Goodsell DS, Forli S,
Protein Science, 2023
2022
Performance evaluation of flexible macrocycle docking in AutoDock
Holcomb M, Santos-Martins D, Tillack AF, Forli S
QRB Discovery, 2022
Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking
Solis-Vasquez L, Tillack AF, Santos-Martins D, Koch A, LeGrand S, Forli S
Parallel Computing, 2022
Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors
Cheng YC, Li G, Smedley CJ, Giel MC, Kitamura S, Woehl J, Bianco G, Forli S, Homer JA, Cappiello JR, Wolan DW, Moses JE, Sharpless KB
Proceeding of the National Academy of Sciences, 2022
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid
Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R
Journal of Computer-Aided Molecular Design, 2022
2021
Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking
Solis-Vasquez L, Tillack AF, Santos-Martins D, Koch A, LeGrand S, Forli S
Parallel Computing, 2021
AutoDock Vina 1.2.0: New docking methods, expanded force field, and Python bindings
Eberhardt J, Santos-Martins D, Tillack AF, Forli S
Journal of Chemical Information and Modelling, 2021
Improving Docking Power for Short Peptides Using Random Forest
Sanner MF, Dieguez L, Forli S, Lis E
Journal of Chemical Information and Modelling, 2021
Discovery of potent coumarin-based kinetic stabilizers of amyloidogenic immunoglobulin light chains using structure-based design
Yan, NL, Santos-Martins D, Nair R, Chu A, Wilson IA, Johnson KA, Forli S, Morgan GJ, Petrassi HM, Kelly JW
Journal of Medicinal Chemistry, 2021
Biased docking for protein–ligand pose prediction
Arcon JP, Turjanski AG, Marti MA, Forli S,
Protein-Ligand Interactions in Drug Design, 2021
Accelerating AutoDock4 with GPUs and gradient-based local search
Santos-Martins D, Solis-Vasquez L, Tillack A, Sanner F, Koch A, Forli S
Journal of Chemical Theory and Computation, 2021
2020
Supercomputer-based ensemble docking drug discovery pipeline with application to Covid-19
Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler KG, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen JD, Ellingson S, Forli S, Glazer J, Gumbart JC, Gunnels J, Hernandez O, Irle S, Kneller DW, Kovalevsky A, Larkin J, Lawrence TJ, LeGrand S, Liu, S-H, Mitchell JC, Park G, Parks JM, Pavlova A, Petridis L, Pool 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
Journal of Chemical Information and Modeling, 2020
A strain-specific inhibitor of receptor-bound HIV-1 targets a pocket near the fusion peptide
Ozorowski G, Torres J, Santos-Martins D, Forli S, Ward A
Cell Reports, 2020
Selective and effective: Current progress in computational structure-based drug discovery of targeted covalent inhibitors
Bianco G, Goodsell DS, Forli S
Trends in Pharmacological Sciences, 2020
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A
Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T
Nature Structural & Molecular Biology, 2020
Synthetic, mechanistic, and biological interrogation of Ginkgo biloba chemical space en route to (−)-bilobalide
Demoret RM, Baker MA, Ohtawa M, Chen S, Lam CC, Kohm S, Roberto M, Forli S, Houk KN, Shenvi RA
JACS, 2020 Sep
The AutoDock Suite at 30
Goodsell DS, Sanner M, Olson AJ, Forli S,
Protein Science, 2020 Aug 17 (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
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
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
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
Art and science of the cellular mesoscale
Goodsell DS, Olson AJ, Forli S
Trends in Biochemical Sciences 2020 Mar 21
Charting hydrogen bond anisotropy
Santos-Martins D, Forli S
Journal of Chemical Theory and Computation, 2020 Mar 10
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
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
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
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
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
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
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, 2019 Oct 1
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
Integrative modeling of the HIV-1 ribonucleoprotein complex
Goodsell DS, Jewett A, Olson AJ, Forli S
Plos Computational Biology, 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
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
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
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
“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
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
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
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
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
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
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
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
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
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
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
Charting a path to success in virtual screening
Forli S
Molecules, 2015 Oct 15
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
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
Computational challenges of structure-based approaches applied to HIV
Forli S, Olson AJ
Current Topics In Microbiology and Immunology, 2015
Postdoctoral, Graduate and Undergraduate
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
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
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
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
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
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
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
Epothilones: From discovery to clinical trials
Forli S
Current Topics In Medicinal Chemistry, 2014
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
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
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
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
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
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
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
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
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
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
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
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
