☰

Steffen Lindert, Ph.D. - Publications

Affiliations: 
Vanderbilt University, Nashville, TN 
Tree Info Similar researchers PubMed Report error

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. Journal of Chemical Information and Modeling. PMID 32633957 DOI: 10.1021/Acs.Jcim.0C00452  0.328
2020 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, ... ... Lindert S, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.682
2019 Leelananda SP, Lindert S. Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. Journal of Chemical Information and Modeling. PMID 31872764 DOI: 10.1021/Acs.Jcim.9B00932  0.404
2019 Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen TH, Di Capua A, 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. Journal of Molecular Biology. PMID 31493410 DOI: 10.1016/J.Jmb.2019.08.017  0.322
2019 Seffernick JT, Harvey SR, Wysocki VH, Lindert S. Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data. Acs Central Science. 5: 1330-1341. PMID 31482115 DOI: 10.1021/Acscentsci.8B00912  0.396
2019 Bowman JD, Lindert S. Computational Studies of Cardiac and Skeletal Troponin. Frontiers in Molecular Biosciences. 6: 68. PMID 31448287 DOI: 10.3389/Fmolb.2019.00068  0.382
2019 Seffernick JT, Ren H, Kim SS, Lindert S. Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder. The Journal of Physical Chemistry. B. PMID 31411026 DOI: 10.1021/Acs.Jpcb.9B04333  0.334
2019 Bowman JD, Coldren WH, Lindert S. Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations. Journal of Chemical Information and Modeling. PMID 31141358 DOI: 10.1021/Acs.Jcim.9B00256  0.332
2019 Aprahamian ML, Lindert S. Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. PMID 30946594 DOI: 10.1021/Acs.Jctc.9B00101  0.305
2019 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30944216 DOI: 10.1073/Pnas.1817632116  0.371
2019 Kim SS, Aprahamian ML, Lindert S. Improving inverse docking target identification with Z-score selection. Chemical Biology & Drug Design. PMID 30604454 DOI: 10.1111/Cbdd.13453  0.312
2018 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. Journal of the American Chemical Society. PMID 30176143 DOI: 10.1021/Jacs.8B06738  0.301
2018 Bowman JD, Lindert S. Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure. The Journal of Physical Chemistry. B. PMID 30070845 DOI: 10.1021/Acs.Jpcb.8B05435  0.321
2018 Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Analytical Chemistry. PMID 29874044 DOI: 10.1021/Acs.Analchem.8B01624  0.386
2018 Kim SS, Seffernick JT, Lindert S. Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. The Journal of Physical Chemistry. B. PMID 29595057 DOI: 10.1021/Acs.Jpcb.8B01763  0.332
2017 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. Journal of Chemical Information and Modeling. PMID 29144742 DOI: 10.1021/acs.jcim.7b00536  0.337
2017 Leelananda SP, Lindert S. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. Journal of Chemical Theory and Computation. PMID 28949136 DOI: 10.1021/Acs.Jctc.7B00464  0.442
2016 Leelananda SP, Lindert S. Computational methods in drug discovery. Beilstein Journal of Organic Chemistry. 12: 2694-2718. PMID 28144341 DOI: 10.3762/Bjoc.12.267  0.321
2016 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. Journal of Molecular and Cellular Cardiology. PMID 27825981 DOI: 10.1016/J.Yjmcc.2016.10.016  0.346
2016 Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S. Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation - An Integrated Multi-Scale Modeling Study. The Journal of Physical Chemistry. B. PMID 27133568 DOI: 10.1021/Acs.Jpcb.6B01950  0.33
2016 Cai F, Li M, Pineda-Sanabria S, Gelozia S, Lindert S, McCammon JA, West F, Sykes B, Hwang P. Designing a High Affinity Cardiac Troponin Activator Biophysical Journal. 110: 465a. DOI: 10.1016/J.Bpj.2015.11.2490  0.31
2016 Lindert S, Marlett M. Cryoem-Guided Iterative Molecular Dynamics - Rosetta Protein Structure Refinement Protocol Improves Protein Model Quality Biophysical Journal. 110: 345a. DOI: 10.1016/J.Bpj.2015.11.1857  0.448
2015 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. The Journal of Biological Chemistry. 290: 27749-66. PMID 26391394 DOI: 10.1074/Jbc.M115.683045  0.302
2015 Lindert S, McCammon JA. Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction. Journal of Chemical Theory and Computation. 11: 1337-46. PMID 25883538 DOI: 10.1021/Ct500995D  0.442
2015 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. Biophysical Journal. 108: 395-407. PMID 25606687 DOI: 10.1016/J.Bpj.2014.11.3461  0.305
2015 Lindert S, Li MX, Sykes BD, McCammon JA. Computer-aided drug discovery approach finds calcium sensitizer of cardiac troponin. Chemical Biology & Drug Design. 85: 99-106. PMID 24954187 DOI: 10.1111/Cbdd.12381  0.322
2014 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. Biophysical Journal. 107: 1675-85. PMID 25296321 DOI: 10.1016/J.Bpj.2014.08.008  0.354
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: E2530-9. PMID 24927548 DOI: 10.1073/Pnas.1409061111  0.322
2014 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. Biochemical and Biophysical Research Communications. 445: 724-33. PMID 24525125 DOI: 10.1016/J.Bbrc.2014.01.179  0.344
2014 Feixas F, Lindert S, Sinko W, McCammon JA. Exploring the role of receptor flexibility in structure-based drug discovery. Biophysical Chemistry. 186: 31-45. PMID 24332165 DOI: 10.1016/J.Bpc.2013.10.007  0.345
2014 Cheng Y, Lindert S, Kekenes-Huskey P, Rao VS, Rosevear PR, McCammon JA, McCulloch A, Regnier M. Exploring How Phosphorylation Influences C-I Interaction and Calcium Sensitivity of Troponin by Molecular Dynamics Simulations Biophysical Journal. 106: 660a. DOI: 10.1016/J.Bpj.2013.11.3654  0.354
2014 Lindert S, McCammon A. Differences in Troponin C Dynamics Between Cardiac and Skeletal Muscle - A Molecular Dynamics Perspective Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.3607  0.343
2014 Regnier M, Cheng Y, Kekenes-Huskey P, Lindert S, McCulloch A. Experimental and Computational Approaches to Study Myofilament Structure-Function in Normal and Diseased Muscle Biophysical Journal. 106: 221a. DOI: 10.1016/J.Bpj.2013.11.1292  0.344
2013 Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. Journal of Chemical Theory and Computation. 9: 4684-4691. PMID 24634618 DOI: 10.1021/Ct400514P  0.327
2013 Lindert S, Meiler J, McCammon JA. Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol to Improve Model Quality. Journal of Chemical Theory and Computation. 9: 3843-3847. PMID 23956701 DOI: 10.1021/Ct400260C  0.56
2013 Durrant JD, Lindert S, McCammon JA. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. Journal of Molecular Graphics & Modelling. 44: 104-12. PMID 23792207 DOI: 10.1016/J.Jmgm.2013.05.006  0.335
2013 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. 526: 318-24. PMID 23732289 DOI: 10.1016/J.Gene.2013.05.027  0.326
2013 Sinko W, Lindert S, McCammon JA. Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chemical Biology & Drug Design. 81: 41-9. PMID 23253130 DOI: 10.1111/Cbdd.12051  0.374
2013 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, et al. Antibacterial drug leads targeting isoprenoid biosynthesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 123-8. PMID 23248302 DOI: 10.1073/Pnas.1219899110  0.304
2013 Lindert S, Stewart PL, Meiler J. Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. Computational Biology and Chemistry. 42: 1-4. PMID 23246775 DOI: 10.1016/J.Compbiolchem.2012.11.001  0.514
2013 Lindert S, Kekenes-Huskey P, McCammon JA. Analysis of Free Energy of Opening the Troponin C Binding Pocket for Troponin I using Microsecond Molecular Dynamics Simulations Biophysical Journal. 104: 331a-332a. DOI: 10.1016/J.Bpj.2012.11.1843  0.334
2013 Rao VS, Lindert S, Wang DD, Kekenes-Huskey P, Cheng Y, McCammon JA, McCulloch A, Arzberger P, Regnier M. Mechanisms of Altered Cardiac Myofibril Relaxation Caused by the Cardiac Troponin-I R145G Mutation Biophysical Journal. 104: 311a. DOI: 10.1016/J.Bpj.2012.11.1728  0.339
2012 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 Computational Biology. 8: e1002777. PMID 23209387 DOI: 10.1371/Journal.Pcbi.1002777  0.34
2012 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. Biophysical Journal. 103: 1784-9. PMID 23083722 DOI: 10.1016/J.Bpj.2012.08.058  0.345
2012 Lindert S, McCammon JA. Dynamics of Plasmodium falciparum enoyl-ACP reductase and implications on drug discovery. Protein Science : a Publication of the Protein Society. 21: 1734-45. PMID 22969045 DOI: 10.1002/Pro.2155  0.332
2012 Lindert S, Durrant JD, McCammon JA. LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chemical Biology & Drug Design. 80: 358-65. PMID 22594624 DOI: 10.1111/J.1747-0285.2012.01414.X  0.321
2012 Lindert S, Alexander N, Wötzel N, Karaka? M, Stewart PL, Meiler J. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. Structure (London, England : 1993). 20: 464-78. PMID 22405005 DOI: 10.1016/J.Str.2012.01.023  0.541
2012 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. The Journal of Physical Chemistry. B. 116: 8449-59. PMID 22329450 DOI: 10.1021/Jp212173F  0.335
2012 Lindert S, Hofmann T, Wötzel N, Karaka? M, Stewart PL, Meiler J. Ab initio protein modeling into CryoEM density maps using EM-Fold. Biopolymers. 97: 669-77. PMID 22302372 DOI: 10.1002/Bip.22027  0.553
2012 Lindert S, Kekenes-Huskey P, McCammon JA. Molecular Dynamics and Calcium Binding Studies on Troponin C Biophysical Journal. 102: 39a. DOI: 10.1016/J.Bpj.2011.11.244  0.333
2011 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. Journal of Structural Biology. 175: 264-76. PMID 21565271 DOI: 10.1016/J.Jsb.2011.04.016  0.521
2011 Meiler J, Lindert S, Stewart P. De Novo Atomic-Detail Structure Prediction for Proteins Guided by Medium Resolution Density Maps Microscopy and Microanalysis. 17: 970-971. DOI: 10.1017/S1431927611005721  0.535
2011 Lindert S, Stewart P, Meiler J. Predicting Models for a Domain of DNA-PKcs Microscopy and Microanalysis. 17: 126-127. DOI: 10.1017/S1431927611001504  0.462
2011 Kim R, Flatt J, Lindert S, Williams D, Smith J, Nemerow G, Stewart P. CryoEM Structural Analysis of Defensin Neutralization of Adenovirus Microscopy and Microanalysis. 17: 102-103. DOI: 10.1017/S1431927611001383  0.302
2010 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 Pathogens. 6: e1000959. PMID 20585634 DOI: 10.1371/Journal.Ppat.1000959  0.319
2009 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. Journal of Virology. 83: 11491-501. PMID 19726496 DOI: 10.1128/Jvi.01214-09  0.377
2009 Lindert S, Staritzbichler R, Wötzel N, Karaka? M, Stewart PL, Meiler J. EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure (London, England : 1993). 17: 990-1003. PMID 19604479 DOI: 10.1016/J.Str.2009.06.001  0.533
2009 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. Journal of Virology. 83: 7375-83. PMID 19458007 DOI: 10.1128/Jvi.00331-09  0.349
2009 Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy. Current Opinion in Structural Biology. 19: 218-25. PMID 19339173 DOI: 10.1016/J.Sbi.2009.02.010  0.53
2009 Lindert S, Staritzbichler R, Woetzel N, Karakas M, Stewart P, Meiler J. Cryo-EM Guided de novo Protein Fold Elucidation Biophysical Journal. 96: 654a. DOI: 10.1016/J.Bpj.2008.12.3454  0.564
Show low-probability matches.