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PDF of all the papers are available upon request

2024

• The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics
  Fischer, A-L. M., Tichy, A., Kokot, J., Hoerschinger, V., J., Wild, R., F., Riccabona, J., R., Loeffler, J., R., Waibi, F., Quoika, P., K., Gshwandtner, P., Forli, S., Ward, A.,B., Liedl, K., R., Zacharias, M., Fernández-Quintero, M., L. 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, J.M.; Li, W., Governa, P., Chen, L.Y. Jadhav A. J. Dongre, A., Forli, S. Parker, C.G. Nature Chem Biol, 2024, https://doi.org/10.1038/s41589-023-01514-z
• Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors
  Governa, P., Biagi, M., Manetti, F., Forli, S. RSC Medicinal Chemistrry, 2024, https://doi.org/10.1039/D3MD00649B

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, https://doi.org/10.26434/chemrxiv-2023-19v1v
• Richard Lerner’s Bioinspiration: Biomolecular Visualization and Modeling at Scripps Research
  Olson, A.J., Sanner, M.F., Goodsell, D.S., Forli, S., Israel Journal of Chemistry, 2023, https://doi.org/10.1002/ijch.202300055
• Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR
  Laboute, T., Zucca, S., Holcomb, M., Patil, D.N., Garza, C., Wheatley, B.A., Roy, R.N., Forli, S., Martemyanov, K.A Science, 2023, https://doi.org/10.1126/science.add7150
• WaterKit: thermodynamic profiling of protein hydration sites
  Eberhardt, J., Forli, S., Journal of Chemical Theory and Computation, 2023, https://doi.org/10.1021/acs.jctc.2c01087
• Ringtail: a Python tool for efficient management and storage of virtual screening results
  Hansel-Harris, A., Santos-Martins, D., Bruciaferri, N., Tillack, A. F., Holcomb, M., Forli, S., Journal of Chemical Information and Modeling , 2023, https://doi.org/10.1021/acs.jcim.3c00166
• 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, https://doi.org/10.1021/acscentsci.2c01462
• Evaluation of AlphaFold2 structures as docking targets
  Holcomb, M., Chang, Y-T, Goodsell, D.S, Forli, S. Protein Science , 2023, https://doi.org/10.1002/pro.4530

2022

• Performance evaluation of flexible macrocycle docking in AutoDock
  Holcomb, M., Santos-Martins, D., Tillack, A.F., Forli, S. QRB Discovery , 2022, https://doi.org/10.1017/qrd.2022.18
• Benchmarking the performance of irregular computations in AutoDock-GPU molecular docking
  Solis-Vasquez, L, Tillack, A. F., Santos-Martins, D., Koch, A., LeGrand, S., Forli, S. Parallel Computing , 2022, https://doi.org/10.1016/j.parco.2021.102861
• 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, https://doi.org/10.1073/pnas.2208540119
• 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, https://doi.org/10.1007/s10822-022-00446-5

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, https://doi.org/10.1016/j.parco.2021.102861
• 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, https://doi.org/10.1021/acs.jcim.1c00203
• Improving Docking Power for Short Peptides Using Random Forest
  Sanner, MF, Dieguez, L, Forli, S, Lis, E, Journal of Chemical Information and Modelling, 2021, https://doi.org/10.1021/acs.jcim.1c00573
• 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, https://doi.org/10.1021/acs.jmedchem.1c00339
• Biased Docking for Protein–Ligand Pose Prediction
  Arcon JP, Turjanski AG, Marti MA, Forli S, Protein-Ligand Interactions in Drug Design, 2021, https://doi.org/10.1007/978-1-0716-1209-5_3
• 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, https://doi.org/10.1021/acs.jctc.0c01006

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, doi.org/10.1021/acs.jcim.0c01010
• 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, doi.org/10.1016/j.celrep.2020.108428
• 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, doi.org:10.1016/j.tips.2020.10.005
• 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, doi.org:10.1038/s41594-020-00520-2
• 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, doi.org:10.1021/jacs.0c08231
• 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
  Goodsell, D.S, Olson, A.J., Forli, S, 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, 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, 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

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, 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