Steffen Lindert

Publications:

Sharma A, Choudhary S, Misra SK, Shami AA, Mishra SK, Drake ZC, Lindert S, Sharp JS. Multidose Inline Size-Exclusion Chromatography-Flash Oxidation for Structural Analysis of Dynamic Protein-Ligand Interactions of Antithrombin III and Unfractionated Heparin. Anal Chem. 2026 Mar 03; 98(8):6045-6055. view on PubMed

Narayanasamy A, Drake ZC, Turzo SMBA, Rolland AD, Prell JS, Wysocki VH, Lindert S. Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction. bioRxiv. 2026 Feb 16. view on PubMed

Drake ZC, Day EH, Toth PD, Lindert S. Deep-learning structure elucidation from single-mutant deep mutational scanning. Nat Commun. 2025 Jul 25; 16(1):6874. view on PubMed

Drake ZC, Fowler AG, Blum AA, Lindert S. Enhanced Protein Complex Prediction via Rosetta, AlphaFold, and Nondifferential Covalent Labeling Mass Spectrometry. J Phys Chem B. 2025 Jul 03; 129(26):6489-6497. view on PubMed

Day EH, Lindert S. Extracting Residue Solvent Exposure from Covalent Labeling Data with Machine Learning: A Hybrid Approach for Protein Structure Prediction. J Am Soc Mass Spectrom. 2025 Jun 04; 36(6):1336-1347. view on PubMed

Toth PD, Ratigan SC, Powell JW, Cassel SR, Yalowich JC, McElroy CA, Lindert S, Bell CE, Mitton-Fry MJ. Structural and Mechanistic Insights into Atypical Bacterial Topoisomerase Inhibitors. ACS Med Chem Lett. 2025 Apr 10; 16(4):660-667. view on PubMed

Bolz RM, Seffernick JT, Drake ZC, Harvey SR, Wysocki VH, Lindert S. Energy Resolved Mass Spectrometry Data from Surfaced Induced Dissociation Improves Prediction of Protein Complex Structure. Anal Chem. 2025 Feb 04; 97(4):2375-2383. view on PubMed

Han D, Spehar JM, Richardson DS, Leelananda S, Chakravarthy P, Grecco S, Reardon J, Stover DG, Bennett C, Sizemore GM, Li Z, Lindert S, Sizemore ST. The RAL Small G Proteins Are Clinically Relevant Targets in Triple Negative Breast Cancer. Cancers (Basel). 2024 Aug 31; 16(17). view on PubMed

Powell JW, Mann CA, Toth PD, Nolan S, Steinert A, Ove C, Seffernick JT, Wozniak DJ, Kebriaei R, Lindert S, Osheroff N, Yalowich JC, Mitton-Fry MJ. Development of Novel Bacterial Topoisomerase Inhibitors Assisted by Computational Screening. ACS Med Chem Lett. 2024 Aug 08; 15(8):1287-1297. view on PubMed

Higgins WT, Vibhute S, Bennett C, Lindert S. Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods. J Chem Inf Model. 2024 01 22; 64(2):435-448. view on PubMed

Turzo SMBA, Seffernick JT, Lyskov S, Lindert S. Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver. Brief Bioinform. 2023 09 20; 24(5). view on PubMed

Shafaattalab S, Li AY, Jayousi F, Maaref Y, Dababneh S, Hamledari H, Baygi DH, Barszczewski T, Ruprai B, Jannati S, Nagalingam R, Cool AM, Langa P, Chiao M, Roston T, Solaro RJ, Sanatani S, Toepfer C, Lindert S, Lange P, Tibbits GF. Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C+/- During Development. bioRxiv. 2023 Aug 13. view on PubMed

Kovvali S, Gao Y, Cool A, Lindert S, Wysocki VH, Bell CE, Gopalan V. Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine. Protein Sci. 2023 07; 32(7):e4695. view on PubMed

Cool AM, Lindert S. Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations. J Chem Inf Model. 2023 06 12; 63(11):3534-3543. view on PubMed

Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship. J Chem Inf Model. 2023 06 12; 63(11):3462-3473. view on PubMed

Hantz ER, Tikunova SB, Belevych N, Davis JP, Reiser PJ, Lindert S. Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscle and Structure Activity Relationship. bioRxiv. 2023 Feb 06. view on PubMed

Drake ZC, Seffernick JT, Lindert S. Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling. Nat Commun. 2022 12 21; 13(1):7846. view on PubMed

Hantz ER, Lindert S. Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C. J Chem Inf Model. 2022 Dec 12; 62(23):6201-6208. view on PubMed

Hantz ER, Lindert S. 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. 2022 11 28; 62(22):5675-5687. view on PubMed

Cool AM, Lindert S. Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin. J Chem Inf Model. 2022 11 28; 62(22):5666-5674. view on PubMed

He J, Turzo SBA, Seffernick JT, Kim SS, Lindert S. Prediction of Intrinsic Disorder Using Rosetta ResidueDisorder and AlphaFold2. J Phys Chem B. 2022 10 27; 126(42):8439-8446. view on PubMed

Thirugnanasambantham P, Kovvali S, Cool A, Gao Y, Sabag-Daigle A, Boulanger EF, Mitton-Fry M, Capua AD, Behrman EJ, Wysocki VH, Lindert S, Ahmer BMM, Gopalan V. Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target. Pathogens. 2022 Sep 26; 11(10). view on PubMed

Turzo SBA, Hantz ER, Lindert S. Applications of machine learning in computer-aided drug discovery. QRB Discov. 2022; 3:e14. view on PubMed

Rayani K, Hantz ER, Haji-Ghassemi O, Li AY, Spuches AM, Van Petegem F, Solaro RJ, Lindert S, Tibbits GF. The effect of Mg2+ on Ca2+ binding to cardiac troponin C in hypertrophic cardiomyopathy associated TNNC1 variants. FEBS J. 2022 12; 289(23):7446-7465. view on PubMed

Turzo SMBA, Seffernick JT, Rolland AD, Donor MT, Heinze S, Prell JS, Wysocki VH, Lindert S. Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction. Nat Commun. 2022 07 28; 13(1):4377. view on PubMed

Seffernick JT, Turzo SBA, Harvey SR, Kim Y, Somogyi Á, Marciano S, Wysocki VH, Lindert S. Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation. Anal Chem. 2022 07 26; 94(29):10506-10514. view on PubMed

Khaje NA, Eletsky A, Biehn SE, Mobley CK, Rogals MJ, Kim Y, Mishra SK, Doerksen RJ, Lindert S, Prestegard JH, Sharp JS. Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol. 2022 05 12; 5(1):452. view on PubMed

Biehn SE, Picarello DM, Pan X, Vachet RW, Lindert S. Accounting for Neighboring Residue Hydrophobicity in Diethylpyrocarbonate Labeling Mass Spectrometry Improves Rosetta Protein Structure Prediction. J Am Soc Mass Spectrom. 2022 Mar 02; 33(3):584-591. view on PubMed

Nguyen TT, Marzolf DR, Seffernick JT, Heinze S, Lindert S. Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR. Structure. 2022 02 03; 30(2):313-320.e3. view on PubMed

Biehn SE, Lindert S. Protein Structure Prediction with Mass Spectrometry Data. Annu Rev Phys Chem. 2022 04 20; 73:1-19. view on PubMed

Lu Y, Vibhute S, Li L, Okumu A, Ratigan SC, Nolan S, Papa JL, Mann CA, English A, Chen A, Seffernick JT, Koci B, Duncan LR, Roth B, Cummings JE, Slayden RA, Lindert S, McElroy CA, Wozniak DJ, Yalowich J, Mitton-Fry MJ. 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. 2021 10 28; 64(20):15214-15249. view on PubMed

Cool AM, Lindert S. Computational Methods Elucidate Consequences of Mutations and Post-translational Modifications on Troponin I Effective Concentration to Troponin C. J Phys Chem B. 2021 07 15; 125(27):7388-7396. view on PubMed

Hantz ER, Lindert S. Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C. J Chem Inf Model. 2021 06 28; 61(6):3052-3057. view on PubMed

Biehn SE, Limpikirati P, Vachet RW, Lindert S. Utilization of Hydrophobic Microenvironment Sensitivity in Diethylpyrocarbonate Labeling for Protein Structure Prediction. Anal Chem. 2021 06 15; 93(23):8188-8195. view on PubMed

Seffernick JT, Canfield SM, Harvey SR, Wysocki VH, Lindert S. Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy. Anal Chem. 2021 06 01; 93(21):7596-7605. view on PubMed

Marzolf DR, Seffernick JT, Lindert S. Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data. J Chem Theory Comput. 2021 Apr 13; 17(4):2619-2629. view on PubMed

Rayani K, Seffernick J, Li AY, Davis JP, Spuches AM, Van Petegem F, Solaro RJ, Lindert S, Tibbits GF. Binding of calcium and magnesium to human cardiac troponin C. J Biol Chem. 2021 Jan-Jun; 296:100350. view on PubMed

Biehn SE, Lindert S. Accurate protein structure prediction with hydroxyl radical protein footprinting data. Nat Commun. 2021 01 12; 12(1):341. view on PubMed

Kim SS, Alves MJ, Gygli P, Otero J, Lindert S. Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex. Curr Comput Aided Drug Des. 2021; 17(1):57-68. view on PubMed

Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys. 2020 Dec 28; 153(24):240901. view on PubMed

Lu Y, Papa JL, Nolan S, English A, Seffernick JT, Shkolnikov N, Powell J, Lindert S, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus. ACS Med Chem Lett. 2020 Dec 10; 11(12):2446-2454. view on PubMed

Coldren WH, Tikunova SB, Davis JP, Lindert S. Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach. J Chem Inf Model. 2020 07 27; 60(7):3648-3661. view on PubMed

Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 07; 17(7):665-680. view on PubMed

Leelananda SP, Lindert S. Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. J Chem Inf Model. 2020 05 26; 60(5):2522-2532. view on PubMed

Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen TH, Capua AD, Bell CE, Ahmer BMM, Lindert S, Wysocki VH, Gopalan V. Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase. J Mol Biol. 2019 11 08; 431(22):4497-4513. view on PubMed

Seffernick JT, Ren H, Kim SS, Lindert S. Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder. J Phys Chem B. 2019 08 22; 123(33):7103-7112. view on PubMed

Bowman JD, Lindert S. Computational Studies of Cardiac and Skeletal Troponin. Front Mol Biosci. 2019; 6:68. view on PubMed

Seffernick JT, Harvey SR, Wysocki VH, Lindert S. Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data. ACS Cent Sci. 2019 Aug 28; 5(8):1330-1341. view on PubMed

Bowman JD, Coldren WH, Lindert S. Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations. J Chem Inf Model. 2019 06 24; 59(6):2964-2972. view on PubMed

Li L, Okumu AA, Nolan S, English A, Vibhute S, Lu Y, Hervert-Thomas K, Seffernick JT, Azap L, Cole SL, Shinabarger D, Koeth LM, Lindert S, Yalowich JC, Wozniak DJ, Mitton-Fry MJ. 1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis. 2019 07 12; 5(7):1115-1128. view on PubMed

Aprahamian ML, Lindert S. Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta. J Chem Theory Comput. 2019 May 14; 15(5):3410-3424. view on PubMed

Harvey SR, Seffernick JT, Quintyn RS, Song Y, Ju Y, Yan J, Sahasrabuddhe AN, Norris A, Zhou M, Behrman EJ, Lindert S, Wysocki VH. Relative interfacial cleavage energetics of protein complexes revealed by surface collisions. Proc Natl Acad Sci U S A. 2019 04 23; 116(17):8143-8148. view on PubMed

Kim SS, Aprahamian ML, Lindert S. Improving inverse docking target identification with Z-score selection. Chem Biol Drug Des. 2019 06; 93(6):1105-1116. view on PubMed

Rhodes CA, Dougherty PG, Cooper JK, Qian Z, Lindert S, Wang QE, Pei D. Cell-Permeable Bicyclic Peptidyl Inhibitors against NEMO-IκB Kinase Interaction Directly from a Combinatorial Library. J Am Chem Soc. 2018 09 26; 140(38):12102-12110. view on PubMed

Bowman JD, Lindert S. Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure. J Phys Chem B. 2018 08 16; 122(32):7874-7883. view on PubMed

Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem. 2018 06 19; 90(12):7721-7729. view on PubMed

Kim SS, Seffernick JT, Lindert S. Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. J Phys Chem B. 2018 04 12; 122(14):3920-3930. view on PubMed

Aprahamian ML, Tikunova SB, Price MV, Cuesta AF, Davis JP, Lindert S. 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. 2017 12 26; 57(12):3056-3069. view on PubMed

Leelananda SP, Lindert S. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. J Chem Theory Comput. 2017 Oct 10; 13(10):5131-5145. view on PubMed

Schwebach CL, Agrawal R, Lindert S, Kudryashova E, Kudryashov DS. The Roles of Actin-Binding Domains 1 and 2 in the Calcium-Dependent Regulation of Actin Filament Bundling by Human Plastins. J Mol Biol. 2017 08 04; 429(16):2490-2508. view on PubMed

Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein J Org Chem. 2016; 12:2694-2718. view on PubMed

Cai F, Li MX, Pineda-Sanabria SE, Gelozia S, Lindert S, West F, Sykes BD, Hwang PM. Structures reveal details of small molecule binding to cardiac troponin. J Mol Cell Cardiol. 2016 Dec; 101:134-144. view on PubMed

Cheng Y, Lindert S, Oxenford L, Tu AY, McCulloch AD, Regnier M. Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation. J Phys Chem B. 2016 08 25; 120(33):8238-53. view on PubMed

Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S. Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study. J Phys Chem B. 2016 08 25; 120(33):8264-75. view on PubMed

Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A. 2015 Dec 22; 112(51):E7073-82. view on PubMed

Cheng Y, Rao V, Tu AY, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation. J Biol Chem. 2015 Nov 13; 290(46):27749-66. view on PubMed

Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. J Chem Theory Comput. 2015 Mar 10; 11(3):1337-46. view on PubMed

Lindert S, Cheng Y, Kekenes-Huskey P, Regnier M, McCammon JA. Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations. Biophys J. 2015 Jan 20; 108(2):395-407. view on PubMed

Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des. 2015 Jun; 85(6):756-69. view on PubMed

Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. J Comput Aided Mol Des. 2015 Jan; 29(1):79-87. view on PubMed

Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Solaro RJ, Rosevear PR, Amaro R, McCulloch AD, McCammon JA, Regnier M. Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics. Biophys J. 2014 Oct 07; 107(7):1675-85. view on PubMed

Rao V, Cheng Y, Lindert S, Wang D, Oxenford L, McCulloch AD, McCammon JA, Regnier M. PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils. Biophys J. 2014 Sep 02; 107(5):1196-1204. view on PubMed

Zinsser VL, Lindert S, Banford S, Hoey EM, Trudgett A, Timson DJ. UDP-galactose 4'-epimerase from the liver fluke, Fasciola hepatica: biochemical characterization of the enzyme and identification of inhibitors. Parasitology. 2015 Mar; 142(3):463-72. view on PubMed

Lindert S, Li MX, Sykes BD, McCammon JA. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chem Biol Drug Des. 2015 Feb; 85(2):99-106. view on PubMed

Liu YL, Lindert S, Zhu W, Wang K, McCammon JA, Oldfield E. Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site. Proc Natl Acad Sci U S A. 2014 Jun 24; 111(25):E2530-9. view on PubMed

Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput. 2014 Apr 08; 10(4):1631-1637. view on PubMed

Lindert S, Maslennikov I, Chiu EJ, Pierce LC, McCammon JA, Choe S. Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits. Biochem Biophys Res Commun. 2014 Mar 21; 445(4):724-33. view on PubMed

Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem. 2014 Feb; 186:31-45. view on PubMed

Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. J Chem Theory Comput. 2013 Nov 12; 9(11):4684-4691. view on PubMed

Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. J Chem Theory Comput. 2013 Aug 13; 9(8):3843-3847. view on PubMed

Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chem Biol Drug Des. 2013 Jun; 81(6):742-8. view on PubMed

Timson DJ, Lindert S. Comparison of dynamics of wildtype and V94M human UDP-galactose 4-epimerase-A computational perspective on severe epimerase-deficiency galactosemia. Gene. 2013 Sep 10; 526(2):318-24. view on PubMed

Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model. 2013 Jul; 44:104-12. view on PubMed

Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des. 2013 Jan; 81(1):41-9. view on PubMed

Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA, Oldfield E. Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):123-8. view on PubMed

Kekenes-Huskey PM, Lindert S, McCammon JA. Molecular basis of calcium-sensitizing and desensitizing mutations of the human cardiac troponin C regulatory domain: a multi-scale simulation study. PLoS Comput Biol. 2012; 8(11):e1002777. view on PubMed

Lindert S, Stewart PL, Meiler J. Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Comput Biol Chem. 2013 Feb; 42:1-4. view on PubMed

Lindert S, Kekenes-Huskey PM, McCammon JA. Long-timescale molecular dynamics simulations elucidate the dynamics and kinetics of exposure of the hydrophobic patch in troponin C. Biophys J. 2012 Oct 17; 103(8):1784-9. view on PubMed

Lindert S, McCammon JA. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Sci. 2012 Nov; 21(11):1734-45. view on PubMed

Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chem Biol Drug Des. 2012 Sep; 80(3):358-65. view on PubMed

Lindert S, Alexander N, Wötzel N, Karakas M, Stewart PL, Meiler J. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure. 2012 Mar 07; 20(3):464-78. view on PubMed

Lindert S, Kekenes-Huskey PM, Huber G, Pierce L, McCammon JA. Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B. 2012 Jul 26; 116(29):8449-59. view on PubMed

Lindert S, Hofmann T, Wötzel N, Karakas M, Stewart PL, Meiler J. Ab initio protein modeling into CryoEM density maps using EM-Fold. Biopolymers. 2012 Sep; 97(9):669-77. view on PubMed

Woetzel N, Lindert S, Stewart PL, Meiler J. BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J Struct Biol. 2011 Sep; 175(3):264-76. view on PubMed

Smith JG, Silvestry M, Lindert S, Lu W, Nemerow GR, Stewart PL. Insight into the mechanisms of adenovirus capsid disassembly from studies of defensin neutralization. PLoS Pathog. 2010 Jun 24; 6(6):e1000959. view on PubMed

Lindert S, Silvestry M, Mullen TM, Nemerow GR, Stewart PL. Cryo-electron microscopy structure of an adenovirus-integrin complex indicates conformational changes in both penton base and integrin. J Virol. 2009 Nov; 83(22):11491-501. view on PubMed

Lindert S, Staritzbichler R, Wötzel N, Karakas M, Stewart PL, Meiler J. EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure. 2009 Jul 15; 17(7):990-1003. view on PubMed

Silvestry M, Lindert S, Smith JG, Maier O, Wiethoff CM, Nemerow GR, Stewart PL. Cryo-electron microscopy structure of adenovirus type 2 temperature-sensitive mutant 1 reveals insight into the cell entry defect. J Virol. 2009 Aug; 83(15):7375-83. view on PubMed

Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy. Curr Opin Struct Biol. 2009 Apr; 19(2):218-25. view on PubMed