Steffen Lindert, Ph.D. - Publications

Vanderbilt University, Nashville, TN 

36 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 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  0.92
2015 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, et al. Antiinfectives targeting enzymes and the proton motive force. Proceedings of the National Academy of Sciences of the United States of America. 112: E7073-82. PMID 26644565 DOI: 10.1073/pnas.1521988112  0.4
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  0.4
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  0.4
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  0.4
2015 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. Chemical Biology & Drug Design. 85: 756-69. PMID 25352216 DOI: 10.1111/cbdd.12463  0.92
2015 Lindert S, Tallorin L, Nguyen QG, Burkart MD, McCammon JA. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors. Journal of Computer-Aided Molecular Design. 29: 79-87. PMID 25344312 DOI: 10.1007/s10822-014-9806-3  0.4
2015 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. 142: 463-72. PMID 25124392 DOI: 10.1017/S003118201400136X  0.92
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  0.4
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  0.4
2014 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. Biophysical Journal. 107: 1196-204. PMID 25185555 DOI: 10.1016/j.bpj.2014.07.027  0.4
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  0.4
2014 Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. Journal of Chemical Theory and Computation. 10: 1631-1637. PMID 24803868 DOI: 10.1021/ct401049q  0.4
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  0.4
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  0.4
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  0.4
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  0.92
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  0.4
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  0.92
2013 Lindert S, Zhu W, Liu YL, Pang R, Oldfield E, McCammon JA. Farnesyl diphosphate synthase inhibitors from in silico screening. Chemical Biology & Drug Design. 81: 742-8. PMID 23421555 DOI: 10.1111/cbdd.12121  0.4
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  0.4
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  0.4
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  0.92
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  0.92
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  0.4
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  0.4
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  0.4
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  0.92
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  0.4
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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/  0.92
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