CosolvKit: A versatile tool for cosolvent MD preparation and analysis

Bruciaferri N, Eberhardt J, Llanos MA, Loeffler JR, Holcomb M, Fernandez-Quintero ML, Santos-Martins D, Ward AB, Forli S

Journal of Chemical Information and Modeling, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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