IP6, PF74 affect HIV-1 capsid stability through modulation of hexamer-hexamer tilt angle preference

Garza CM, Holcomb M, Santos-Martins D, Torbett BE, Forli S

Biophysical Journal, 2025

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 A-LM, 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

Enhanced mapping of small-molecule binding sites in cells

Wozniak JM, Li W, Governa P, Chen L-Y, Jadhav A, Dongre A, Forli S, Parker CG

Nature Chemical Biology, 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

The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics

Fischer A-LM, Tichy A, Kokot J, Hoerschinger VJ, Wild RF, Riccabona JR, Loeffler JR, Waibl F, Quoika PK, Gschwandtner P, Forli S, Ward AB, Liedl KR, Zacharias M, Fernández-Quintero ML

Journal of Chemical Theory and Computation, 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, Tillack A, Hansel-Harris A, Forli S

Journal of Chemical Information and Modeling, 2023

WaterKit: Thermodynamic Profiling of Protein Hydration Sites

Eberhardt J, Forli S

Journal of Chemical Theory and Computation, 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

Stretching Peptides to Generate Small Molecule β-Strand Mimics

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

ACS Central Science, 2023

Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results

Hansel-Harris AT, Santos-Martins D, Bruciaferri N, Tillack AF, Holcomb M, Forli S

Journal of Chemical Information and Modeling, 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

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

Diversity oriented clicking delivers β-substituted alkenyl sulfonyl fluorides as covalent human neutrophil elastase inhibitors

Cheng Y, Li G, Smedley CJ, Giel M-C, Kitamura S, Woehl JL, Bianco G, Forli S, Homer JA, Cappiello JR, Wolan DW, Moses JE, Sharpless KB

Proceedings of the National Academy of Sciences, 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

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

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 Modeling, 2021

Improving Docking Power for Short Peptides Using Random Forest

Sanner MF, Dieguez L, Forli S, Lis E

Journal of Chemical Information and Modeling, 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

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

Santos-Martins D, Solis-Vasquez L, Tillack AF, Sanner MF, Koch A, Forli S

Journal of Chemical Theory and Computation, 2021

Biased Docking for Protein–Ligand Pose Prediction

Arcon JP, Turjanski AG, Martí MA, Forli S

Protein-Ligand Interactions and Drug Design, 2021

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

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

Journal of Chemical Information and Modeling, 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

A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide

Ozorowski G, Torres JL, Santos-Martins D, Forli S, Ward AB

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

Synthetic, Mechanistic, and Biological Interrogation of Ginkgo biloba Chemical Space En Route to (−)-Bilobalide

Demoret RM, Baker MA, Ohtawa M, Chen S, Lam CC, Khom S, Roberto M, Forli S, Houk KN, Shenvi RA

Journal of the American Chemical Society, 2020

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

The AutoDock suite at 30

Goodsell DS, Sanner MF, Olson AJ, Forli S

Protein Science, 2021

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

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

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

Charting Hydrogen Bond Anisotropy

Santos-Martins D, Forli S

Journal of Chemical Theory and Computation, 2020

Art and Science of the Cellular Mesoscale

Goodsell DS, Olson AJ, Forli S

Trends in Biochemical Sciences, 2020

Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity

Xu JH, Eberhardt J, Hill-Payne B, González-Páez GE, Castellón JO, Cravatt BF, Forli S, Wolan DW, Backus KM

ACS Chemical Biology, 2020

Structural basis for strand-transfer inhibitor binding to HIV intasomes

Passos DO, Li M, Jóźwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke TR, Craigie R, Lyumkis D

Science, 2020

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

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

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

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

Nature Chemistry, 2019

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, 2019

AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools

Zhang Y, Forli S, Omelchenko A, Sanner MF

Journal of Computational Chemistry, 2019

Integrative modeling of the HIV-1 ribonucleoprotein complex

Goodsell DS, Jewett A, Olson AJ, Forli S

PLOS Computational Biology, 2019

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

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

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

Journal of Medicinal Chemistry, 2019

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 Advances, 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

“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

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

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

Journal of Biological Chemistry, 2016

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

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 C-T, Dutta SK, Geralt M, Wüthrich K, Adams JA

Journal of Molecular Biology, 2016

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

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 JJP, Nizet V

Journal of Biological Chemistry, 2016

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

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

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

Bianco G, Forli S, Goodsell DS, Olson AJ

Protein Science, 2016

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

Charting a Path to Success in Virtual Screening

Forli S

Molecules, 2015

A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA

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

Journal of Chemical Information and Modeling, 2015

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 RSK, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM

The Journal of Physical Chemistry B, 2015

Computational Challenges of Structure-Based Approaches Applied to HIV

Forli S, Olson AJ

Current Topics in Microbiology and Immunology, 2015

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, Catalan FV, 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

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

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

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, Santos-Martins D, Olson AJ

Journal of Computer-Aided Molecular Design, 2014

Epothilones: From Discovery to Clinical Trials

Forli S

Current Topics in Medicinal Chemistry, 2014

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

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 Y-C, Perryman AL, Rhee J-K, 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

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

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

The Journal of Organic Chemistry, 2011

Virtual screening with AutoDock: theory and practice

Cosconati S, Stefano F, L. PA, Rodney H, S. GD, and Olson AJ

Expert Opinion on Drug Discovery, 2010

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

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

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 K-H, Botta M

ChemMedChem, 2010

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, Torre FL, Anzini M, Patrignani P

Bioorganic & Medicinal Chemistry, 2008

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

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

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

3D QSAR studies of the interaction between β-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

Il Farmaco, 2003