Publications

  1. Higgins, W.T.; Vibhute, S.; Bennett, C.; Lindert, S. (2024), Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. J Chem Inf Model 64 (2), 435-448. (Abstract | PubMed | PDF)
  2. Turzo, S.B.A.; Seffernick, J.T.; Lyskov, S.; Lindert, S. (2023), Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver. Brief Bioinform 24 (5), bbad308. (Abstract | PubMed | PDF)
  3. Kovvali, S.; Gao, Y.; Cool, A.M.; Lindert, S.; Wysocki, V.H.; Bell, C.E.; Gopalan, V. (2023), Insights Into The Catalytic Mechanism of A Bacterial Deglycase Essential For Utilization of Fructose-Lysine. Protein Sci 32 (7), e4695. (Abstract | PubMed | PDF)
  4. Cool, A.M.; Lindert, S. (2023), Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. J Chem Inf Model 63 (11), 3534-3543. (Abstract | PubMed | PDF)
  5. Hantz, E.R.; Tikunova, S.B.; Belevych, N.; Davis, J.P.; Reiser, P. J.; Lindert, S. (2023), Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. J Chem Inf Model 63 (11), 3462-3473. (Abstract | PubMed | PDF)
  6. Drake, Z.C.; Seffernick, J.T.; Lindert, S. (2022), Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling. Nat Commun 13 (1), 7846. (Abstract | PubMed | PDF)
  7. Hantz, E.R.; Lindert, S. (2022), Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. J Chem Inf Model 62 (23), 6201-6208. (Abstract | PubMed | PDF)
  8. Hantz, E.R.; Lindert, S. (2022), Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors. J Chem Inf Model 62 (22), 5675-5687. (Abstract | PubMed | PDF)
  9. Turzo, S.B.A.; Hantz, E.R.; Lindert, S. (2022), Applications of machine learning in computer-aided drug discovery. QRB Discov 3, e14. (Abstract | PubMed | PDF)
  10. Thirugnanasambantham, P.; Kovvali, S.; Cool, A.M.; Gao, Y.; Sabag-Daigle, A.; Boulanger, E.F.; Mitton-Fry, M.J.; Capua, A.D.; Behrman, E.J.; Wysocki, V.H.; Lindert, S.; Ahmer, B.M.M.; Gopalan, V. (2022), Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target. Pathogens 11 (10), 1102. (Abstract | PubMed | PDF)
  11. Cool, A.M.; Lindert, S. (2022), Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. J Chem Inf Model 62 (22), 5666-5674. (Abstract | PubMed | PDF)
  12. He, J.; Turzo, S.B.A.; Seffernick, J.T.; Kim, S.S.; Lindert, S. (2022), Prediction of Intrinsic Disorder Using Rosetta ResidueDisorder and AlphaFold2. J Phys Chem B 126 (42), 8439-8446. (Abstract | PubMed | PDF)
  13. Turzo, S.B.A.; Seffernick, J.T.; Rolland, A.D.; Donor, M.T.; Heinze, S.; Prell, J.S.; Wysocki, V.H.; Lindert, S. (2022), Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction. Nat Commun 13 (1), 4377. (Abstract | PubMed | PDF)
  14. Rayani, K.; Hantz, E.R.; Haji-Ghassemi, O.; Li, A.Y.; Spuches, A.M.; Van Petegem, F.; Solaro, R.J.; Lindert, S.; Tibbits, G.F. (2022), The effect of Mg2+ on Ca2+ binding to cardiac troponin C in hypertrophic cardiomyopathy associated TNNC1 variants. FEBS J 289 (23), 7446-7465. (Abstract | PubMed | PDF)
  15. Seffernick, J.T.; Turzo, S.B.A.; Harvey, S.R.; Kim, Y.; Somogyi, Á.; Marciano, S.; Wysocki, V.H.; Lindert, S. (2022), Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation. Anal Chem 94 (29), 10506-10514. (Abstract | PubMed | PDF)
  16. Khaje, N.A.; Eletsky, A.; Biehn, S.E.; Mobley, C.K.; Rogals, M.J.; Kim, Y.; Mishra, S.K.; Doerksen, R.J.; Lindert, S.; Prestegard, J.H.; Sharp, J.S. (2022), Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol 5 (1), 452. (Abstract | PubMed | PDF)
  17. Biehn, S.E.; Picarello, D.M., Pan, X.; Vachet, R.W.; Lindert, S. (2022), Accounting for Neighboring Residue Hydrophobicity in Diethylpyrocarbonate Labeling Mass Spectrometry Improves Rosetta Protein Structure Prediction. J Am Soc Mass Spectrom 33 (3), 584-591. (Abstract | PubMed | PDF)
  18. Nguyen, T.T.; Marzolf, D.R.; Seffernick, J.T.; Heinze, S.; Lindert, S. (2021), Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR. Structure 30 (2), 313-320. (Abstract | PubMed | PDF)
  19. Biehn, S.E.; Lindert, S. (2021), Protein Structure Prediction with Mass Spectrometry Data. Annu Rev Phys Chem. 73, 1-19. (Abstract | PubMed | PDF)
  20. Lu, Y.; Vibhute, S.; Li, L.; Okumu, A.; Ratigan, S.C.; Nolan, S.; Papa, J.L.; Mann, C.A.; English, A.; Chen, A.; Seffernick, J.T.; Koci, B.; Duncan, L.R.; Roth, B.; Cummings, J.E.; Slayden, R.A.; Lindert, S.; McElroy, C.A.; Wozniak, D.J.; Yalowich, J.; Mitton-Fry, M.J. (2021), Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA. J Med Chem 64 (20), 15214-15249. (Abstract | PubMed | PDF)
  21. Cool, A.M.; Lindert, S. (2021), Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C. J Phys Chem B 125 (27), 7388-7396. (Abstract | PubMed | PDF)
  22. Hantz, E.R.; Lindert, S. (2021), Adaptive Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C. J Chem Inf Model 61 (6), 3052-3057. (Abstract | PubMed | PDF)
  23. Biehn, S.E.; Limpikirati, P.; Vachet, R.W.; Lindert, S. (2021), Utilization of Hydrophobic Microenvironment Sensitivity in Diethylpyrocarbonate Labeling for Protein Structure Prediction. Anal Chem 93 (23), 8188-8195. (Abstract | PubMed | PDF)
  24. Seffernick, J.T.; Canfield, S.M.; Harvey, S.R.; Wysocki, V.H.; Lindert, S. (2021), Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy. Anal Chem 93 (21), 7596–7605. (Abstract | PubMed | PDF)
  25. Marzolf, D.R.; Seffernick, J.T.; Lindert, S. (2021), Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. J Chem Theory Comput 17 (4), 2619-2629. (Abstract | PubMed | PDF)
  26. Rayani, K.; Seffernick, J.T.; Li, A.Y.; Davis, J.P.; Spuches, A.M.; Van Petegem, F.; Solaro, R.J.; Lindert, S.; Tibbits, G.F. (2021), Binding of calcium and magnesium to human cardiac Troponin C. J Biol Chem 296, 100350. (Abstract | PubMed | PDF)
  27. Biehn, S.E.; Lindert, S. (2021), Accurate Protein Structure Prediction with Hydroxyl Radical Protein Footprinting Data. Nat Commun 12, 341. (Abstract | PubMed | PDF)
  28. Kim, S.S.; Alves, M.J.; Gygli, P.; Otero, J.; Lindert, S. (2021), Identification of novel cyclin A2 binding site and nanomolar inhibitors of cyclin A2-CDK2 complex. Curr Comput Aided Drug Des 17 (1), 57-68. (Abstract | PubMed | PDF)
  29. Seffernick, J.T.; Lindert, S. (2020), Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 153 (24), 240901. (Abstract | PubMed | PDF)
  30. Lu, Y.; Papa, J.L.; Nolan, S.; English, A.; Seffernick, J.T.; Shkolnikov, N.; Powell, J.; Lindert, S.; Wozniak, D.J.; Yalowich, J.; Mitton-Fry, M.J. (2020), Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus. ACS Med Chem Lett 11 (12), 2446-2454. (Abstract | PubMed | PDF)
  31. Coldren, W.H.; Tikunova, S.B.; Davis, J.P.; Lindert, S. (2020), Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach. J Chem Inf Model 60 (7), 3648-3661. (Abstract | PubMed | PDF)
  32. Leman, J.K.; Weitzner, B.D.; Lewis, S.M.; Adolf-Bryfogle, J.; Alam, N.; Alford, R.F.; Aprahamian, M.; Baker, D.; Barlow, K.A.; Barth, P.; Basanta, B.; Bender, B.J.; Blacklock, K.; Bonet, J.; Boyken, S.E.; Bradley, P.; Bystroff, C.; Conway, P.; Cooper, S.; Correia, B.E.; Coventry, B.; Das, R.; De Jong, R.M.; DiMaio, F.; Dsilva, L.; Dunbrack, R.; Ford, A.S.; Frenz, B.; Fu, D.Y.; Geniesse, C.; Goldschmidt, L.; Gowthaman, R.; Gray, J.J.; Gront, D.; Guffy, S.; Horowitz, S.; Huang, P.S.; Huber, T.; Jacobs, T.M.; Jeliazkov, J.R.; Johnson, D.K.; Kappel, K.; Karanicolas, J.; Khakzad, H.; Khar, K.R.; Khare, S.D.; Khatib, F.; Khramushin, A.; King, I.C.; Kleffner, R.; Koepnick, B.; Kortemme, T.; Kuenze, G.; Kuhlman, B.; Kuroda, D.; Labonte, J.W.; Lai, J.K.; Lapidoth, G.; Leaver-Fay, A.; Lindert, S.; Linsky, T.; London, N.; Lubin, J.H.; Lyskov, S.; Maguire, J.; Malmström, L.; Marcos, E.; Marcu, O.; Marze, N.A.; Meiler, J.; Moretti, R.; Mulligan, V.K.; Nerli, S.; Norn, C.; Ó’Conchúir, S.; Ollikainen, N.; Ovchinnikov, S.; Pacella, M.S.; Pan, X.; Park, H.; Pavlovicz, R.E.; Pethe, M.; Pierce, B.G.; Pilla, K.B.; Raveh, B.; Renfrew, P.D.; Burman, S.S.R.; Rubenstein, A.; Sauer, M.F.; Scheck, A.; Schief, W.; Schueler-Furman, O.; Sedan, Y.; Sevy, A.M.; Sgourakis, N.G.; Shi, L.; Siegel, J.B.; Silva, D.A.; Smith, S.; Song, Y.; Stein, A.; Szegedy, M.; Teets, F.D.; Thyme, S.B.; Wang, R.Y.; Watkins, A.; Zimmerman, L.; Bonneau, R. (2020), Macromolecular Modeling and Design in Rosetta: Recent Methods and Frameworks. Nat Methods 17 (7), 665-680. (Abstract | PubMed | PDF)
  33. Leelananda, S.P.; Lindert, S. (2020), Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. J Chem Inf Model 60 (5), 2522-2532. (Abstract | PubMed | PDF)
  34. Sengupta, A.; Wu, J.; Seffernick, J.T.; Sabag-Daigle, A.; Thomsen, N.; Chen, T.H.; Di Capua, A.; Bell, C.E.; Ahmer, B.M.M.; Lindert, S.; Wysocki, V.H.; Gopalan, V. (2019), Integrated use of biochemical, native mass spectrometry, computational and genome-editing methods to elucidate the mechanism of a Salmonella deglycase. J Mol Biol 431 (22), 4497-4513. (Abstract | PubMed | PDF)
  35. Seffernick, J.T.; Harvey, S.R.; Wysocki, V.H.; Lindert, S. (2019), Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data. ACS Cent Sci 5 (8), 1330-1341. (Abstract | PubMed | PDF)
  36. Bowman, J.D.; Lindert, S. (2019), Computational Studies of Cardiac and Skeletal Troponin. Front Mol Biosci 6:68. (Abstract | PubMed | PDF)
  37. Seffernick, J.T.; Ren, H.; Kim, S.S.; Lindert, S. (2019), Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder. J Phys Chem B 123 (33), 7103-7112. (Abstract | PubMed | PDF)
  38. Bowman, J.D.; Coldren, W.H.; Lindert, S. (2019), Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations. J Chem Inf Model 59 (6), 2964-2972. (Abstract | PubMed | PDF)
  39. Li, L.; Okumu, A.A.; Nolan, S.; English, A.; Vibhute, S.; Lu, Y.; Hervert-Thomas, K.; Seffernick, J.T.; Azap, L.; Cole, S.L.; Shinabarger, D.; Koeth, L.; Lindert, S.; Yalowich, J.; Wozniak, D.J.; Mitton-Fry, M.J. (2019), 1,3-Dioxane-linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis 5 (7), 1115-1128. (Abstract | PubMed | PDF)
  40. Aprahamian, M.L.; Lindert, S. (2019), Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta. J Chem Theory Comput 15 (5), 3410-3424. (Abstract | PubMed | PDF)
  41. Harvey, S.R.; Seffernick, J.T.; Quintyn, R.S.; Song, Y.; Ju, Y.; Yan, J.; Sahasrabuddhe, A.N.; Norris, A.; Zhou, M.; Behrman, E.J.; Lindert, S.; Wysocki, V.H. (2019), Relative interfacial cleavage energetics of protein complexes revealed by surface collisions. Proc Natl Acad Sci U S A 116 (17), 8143-8148. (Abstract | PubMed | PDF)
  42. Kim, S.S.; Aprahamian, M.L.; Lindert, S. (2019), Improving inverse docking target identification with Z-score selection. Chem Biol Drug Des 93 (6), 1105-1116. (Abstract | PubMed | PDF)
  43. Rhodes, C.A.; Dougherty, P.G.; Cooper, J.K.; Qian, Z.; Lindert, S.; Wang, Q.E.; Pei, D. (2018), Cell-Permeable Bicyclic Peptidyl Inhibitors against NEMO-IκB kinase Interaction Directly from a Combinatorial Library. J Am Chem Soc 140 (38), 12102–12110. (Abstract | PubMed | PDF)
  44. Bowman, J.D.; Lindert, S. (2018), Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure. J Phys Chem B 122 (32), 7874–7883. (Abstract | PubMed | PDF)
  45. Aprahamian, M.L.; Chea, E.E.; Jones, L.M.; Lindert, S. (2018), Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem 90 (12), 7721–7729. (Abstract | PubMed | PDF)
  46. Kim, S.S.; Seffernick, J.T.; Lindert, S. (2018), Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. J Phys Chem B 122 (14), 3920-30. (Abstract | PubMed | PDF)
  47. Aprahamian, M.L.; Tikunova, S.B.; Price, M.V.; Cuesta, A.F.; Davis, J.P.; Lindert, S. (2017), Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders. J Chem Inf Model 57 (12), 3056-3069. (Abstract | PubMed | PDF)
  48. Leelananda, S.P.; Lindert, S. (2017), Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. J Chem Theory Comput 13 (10), 5131-5145. (Abstract | PubMed | PDF)
  49. Schwebach, C.L.; Agrawal, R.; Lindert, S.; Kudryashova, E.; Kudryashov, D.S. (2017), The Roles of Actin-Binding Domains 1 and 2 in the Calcium-Dependent Regulation of Actin Filament Bundling by Human Plastins. J Mol Biol 429 (16), 2490–2508. (Abstract | PubMed | PDF)
  50. Leelananda, S.P.; Lindert, S. (2016), Computational methods in drug discovery. Beilstein J Org Chem 12, 2694–2718. (Abstract | PubMed | PDF)
  51. Cai, F.; Li, M. X.; Pineda-Sanabria, S.E.; Gelozia, S.; Lindert, S.; West, F.; Sykes, B.D.; Hwang, P.M. (2016), Structures reveal details of small molecule binding to cardiac troponin. J Mol Cell Cardiol 101, 134-44. (Abstract | PubMed | PDF)
  52. Dewan, S.; McCabe, K. J.; Regnier, M.; McCulloch, A. D.; Lindert, S. (2016), Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation – An Integrated Multi-Scale Modeling Study. J Phys Chem B 120 (33), 8264-75. (Abstract | PubMed | PDF)
  53. Cheng, Y.; Lindert, S.; Oxenford, L.; Tu, A.Y.; McCulloch, A. D.; Regnier, M. (2016), The Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation. J Phys Chem B 120 (33), 8238-53. (Abstract | PubMed | PDF)
  54. Feng, X.; Zhu, W.; Schurig-Briccio, L.A.; Lindert, S.; Shoen, C.; Hitchings, R.; Li, J.; Wang, Y.; Baig, N.; Zhou, T.; Kim, B.K.; Crick, D.C.; Cynamon , M.; McCammon, J. A.; Gennis , R.B.; Oldfield, E. (2015), Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A 112 (51), E7073-E7082. (Abstract | PubMed | PDF)
  55. Cheng, Y.; Rao, V. S.; Tu, A.Y.; Lindert, S.; Wang, D.; Oxenford, L.; McCulloch, A. D.; McCammon, J. A.; Regnier, M. (2015), Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. J Biol Chem 290 (46), 27749-27766. (Abstract | PubMed | PDF)
  56. Lindert, S.; McCammon, J. A. (2015), Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput 11 (3), 1337–1346. (Abstract | PubMed | PDF)
  57. Lindert, S.; Cheng, Y.; Kekenes-Huskey, P. M.; Regnier, M.; McCammon, J. A. (2015), Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation elucidated by Molecular Dynamics Simulations. Biophys J 108 (2), 395–407. (Abstract | PubMed | PDF)
  58. Lindert, S.; Tallorin, L. C.; Nguyen, Q. G.; Burkart, M.D.; McCammon, J. A. (2015), In silico Screening for Plasmodium falciparum Enoyl-ACP Reductase inhibitors. J Comput Aided Mol Des 29 (1), 79-87. (Abstract | PubMed | PDF)
  59. Lindert, S.; Li, M. X.; Sykes, B.; McCammon, J.A. (2015), Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chem Biol Drug Des 85 (2), 99-106. (Abstract | PubMed | PDF)
    Article featured as Editor’s Choice
  60. Zinsser, V. L.; Lindert, S.; Banford, S.; Hoey, E. M.; Trudgett, A.; Timson, D. J. (2015), UDP-galactose 4′-epimerase from the liver fluke, Fasciola hepatica: biochemical characterisation of the enzyme and identification of inhibitors. Parasitology 142 (3), 463-472. (Abstract | PubMed | PDF)
  61. Kim, M. O.; Feng, X.; Feixas, F.; Wei, Z.; Lindert, S.; Bogue, S.; Sinko, W.; de Oliveira, C.; Rao, G.; Oldfield, E.; McCammon, J. A. (2015), A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility, and Implications for Computer-Aided Drug Discovery. Chem Biol Drug Des 85(6):756-69. (Abstract | PubMed | PDF)
  62. Cheng, Y.; Lindert, S.; Kekenes-Huskey, P. M.; Rao, V. S.; Solaro, R.J.; Rosevear, P.R.; Amaro, R.; McCulloch, A. D.; McCammon, J. A.; Regnier, M. (2014), Computational Studies of S23D/S24D Troponin I Mutation on Cardiac Troponin Structural Dynamics. Biophys J 107 (7), 1675-1685. (Abstract| PubMed | PDF)
  63. Rao, V. S.; Cheng, Y.; Lindert, S.; Wang, D.; Oxenford, L.; McCulloch, A. D.; McCammon, J. A.; Regnier, M. (2014), PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J 107 (5), 1196-1204. (Abstract | PubMed | PDF)
  64. Liu, Y. L.*; Lindert, S.*; Zhu, W.; Wang, K.; McCammon, J. A.; Oldfield, E. (2014), Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A 111 (25), E2530-E2539. (Abstract | PubMed | PDF)
  65. Goetz, A.; Bucher, D.; Lindert, S.; McCammon, J. A. (2014), Dipeptide aggregation in aqueous solution from fixed point-charge force fields. J Chem Theory Comput 10 (4), 1631–1637 (Abstract | PubMed | PDF)
  66. Lindert, S.*; Maslennikov I.*; Chiu E.; Pierce, L.C.; McCammon, J. A.; Choe, S. (2014), Drug screening strategy for human membrane proteins: From NMR protein backbone structure to in silica- and NMR-screened hits. Biochem Biophys Res Commun 445 (4), 724-733 (Abstract | PubMed | PDF)
  67. Feixas, F.; Lindert, S.; Sinko, W.; McCammon, J. A. (2014), Exploring the Role of Receptor Flexibility in Structure-Based Drug Discovery. Biophysical Chemistry 186C, 31-45 (Abstract | PubMed | PDF)
  68. Lindert, S.; Bucher, D.; Eastman, P.; Pande, V.; McCammon, J. A. (2013), Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. J Chem Theory Comput 9 (11), 4684–4691 (Abstract | PubMed | PDF)
  69. Lindert, S.; Meiler, J.; McCammon, J. A. (2013), Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput 9 (8), 3843-3847 (Abstract | PubMed | PDF)
  70. Durrant, J. D.; Lindert, S.; McCammon, J. A. (2013), AutoGrow 3.0: An improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model 44C, 104-112 (Abstract | PubMed | PDF)
  71. Timson, D.; Lindert, S. (2013), Comparison of Dynamics of Wildtype and V94M Human UDP-Galactose 4-Epimerase – A computational perspective on severe Epimerase-deficiency Galactosemia. Gene 526 (2), 318-24 (Abstract | PubMed | PDF)
  72. Lindert, S.; Zhu, W.; Liu, Y. L.; Pang, R.; Oldfield, E.; McCammon, J.A. (2013), Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des 81 (6), 742-8. (Abstract | PubMed | PDF)
  73. Zhu, W.; Zhang, Y.; Sinko, W.; Hensler, M. E.; Olson, J.; Molohon, K. J.; Lindert, S.; Cao, R.; Li, K.; Wang, K.; Wang, Y.; Liu, Y. L.; Sankovsky, A.; de Oliveira, C. A.; Mitchell, D. A.; Nizet, V.; McCammon, J. A.; Oldfield, E. (2013), Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A 110 (1), 123-128. (Abstract | PubMed | PDF)
  74. Sinko, W.; Lindert, S.; McCammon, J. A. (2013), Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design. Chem Biol Drug Des 81 (1), 41-49. (Abstract | PubMed | PDF)
  75. Lindert, S.; Stewart, P. L.; Meiler, J. (2013), Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput Biol Chem 42, 1-4. (Abstract | PubMed | PDF)
  76. Lindert, S.; Kekenes-Huskey, P. M.; McCammon, J. A. (2012). Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J 103 (8), 1784-1789. (Abstract | PubMed | PDF)
  77. Lindert, S. and McCammon, J.A. (2012). Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Sci 21(11): 1734-1745. (Abstract | PubMed | PDF)
  78. Kekenes-Huskey, P. M., Lindert, S. and McCammon, J.A. (2012). Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. PLoS Comput Biol 8(11). (Abstract | PubMed | PDF)
  79. Lindert, S., Kekenes-Huskey, P.M., Huber, G., Pierce, L., and McCammon, J.A. (2012). Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B 116, 8449-8459. (Abstract | PubMed | PDF)
  80. Lindert, S.*, Durrant, J.*, McCammon, J. A. (2012). LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders. Chem Biol Drug Des 80, 358-365. (Abstract | PubMed | PDF)
  81. Lindert, S., Alexander, N., Wotzel, N., Karakas, M., Stewart, P.L., and Meiler, J. (2012). EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps. Structure 20, 464-478. (Abstract | PubMed | PDF)
    Article featured in PSI Nature Structural Biology KB
  82. Lindert, S., Hofmann, T., Wotzel, N., Karakas, M., Stewart, P.L., and Meiler, J. (2012). Ab initio protein modeling into CryoEM density maps using EM-Fold. Biopolymers 97, 669-677. (Abstract | PubMed | PDF)
  83. Woetzel, N., Lindert, S., Stewart, P.L., and Meiler, J. (2011). BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. Journal of Structural Biology 175, 264-276. (Abstract | PubMed | PDF)
  84. Smith JG, Silvestry M, Lindert, S., Lu W, Nemerow GR, et al. (2010) Insight into the Mechanisms of Adenovirus Capsid Disassembly from Studies of Defensin Neutralization. PLoS Pathog 6(6). (Abstract | PubMed | PDF)
  85. Lindert, S., Stewart, P.L., and Meiler, J. (2009). Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol 19, 218-225. (Abstract | PubMed | PDF)
  86. Lindert, S., Staritzbichler, R., Wotzel, N., Karakas, M., Stewart, P.L., and Meiler, J. (2009). EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure 17, 990-1003. (Abstract | PubMed | PDF)
  87. Lindert, S., Silvestry, M., Mullen, T.M., Nemerow, G.R., and Stewart, P.L. (2009). Cryo-electron microscopy structure of an adenovirus-integrin complex indicates conformational changes in both penton base and integrin. J Virol 83, 11491-11501. (Abstract | PubMed | PDF)
  88. Silvestry, M., Lindert, S., Smith, J.G., Maier, O., Wiethoff, C.M., Nemerow, G.R., and Stewart, P.L. (2009). Cryo-electron microscopy structure of adenovirus type 2 temperature-sensitive mutant 1 reveals insight into the cell entry defect. J Virol 83, 7375-7383. (Abstract | PubMed | PDF)

* signifies equal contribution