S. Lindert

发表

Hybrid approaches: applying computational methods in cryo-electron microscopy.

P. Stewart, S. Lindert, J. Meiler, 2009, Current opinion in structural biology.

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer‐Aided Drug Design

J. Mccammon, S. Lindert, W. Sinko, 2013, Chemical biology & drug design.

Exploring the role of receptor flexibility in structure-based drug discovery.

J. Mccammon, S. Lindert, W. Sinko, 2014, Biophysical chemistry.

EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

P. Stewart, S. Lindert, J. Meiler, 2012, Structure.

BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

Jens Meiler, Steffen Lindert, Nils Woetzel, 2011, Journal of structural biology.

Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data

S. Lindert, V. Wysocki, Sophie R. Harvey, 2019, ACS central science.

EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

P. Stewart, S. Lindert, J. Meiler, 2009, Structure.

Ab initio protein modeling into CryoEM density maps using EM-Fold.

P. Stewart, S. Lindert, J. Meiler, 2012, Biopolymers.

Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.

Sumudu P. Leelananda, S. Lindert, 2017, Journal of chemical theory and computation.

Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.

S. Lindert, Melanie L. Aprahamian, Emily E. Chea, 2018, Analytical chemistry.

Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.

S. Lindert, Justin T. Seffernick, Stephanie S. Kim, 2018, The journal of physical chemistry. B.

Relative interfacial cleavage energetics of protein complexes revealed by surface collisions

S. Lindert, V. Wysocki, Andrew S. Norris, 2019, Proceedings of the National Academy of Sciences.

Drug screening strategy for human membrane proteins: from NMR protein backbone structure to in silica- and NMR-screened hits.

Levi C. T. Pierce, J. Mccammon, S. Lindert, 2014, Biochemical and biophysical research communications.

AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design.

J Andrew McCammon, Steffen Lindert, Jacob D Durrant, 2013, Journal of molecular graphics & modelling.

Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.

Steffen Lindert, Melanie L Aprahamian, S. Lindert, 2019, Journal of chemical theory and computation.

Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site

J Andrew McCammon, Steffen Lindert, Wei Zhu, 2014, Proceedings of the National Academy of Sciences.

Insight into the Mechanisms of Adenovirus Capsid Disassembly from Studies of Defensin Neutralization

P. Stewart, G. Nemerow, M. Silvestry, 2010, PLoS pathogens.

Iterative Molecular Dynamics − Rosetta Membrane Protein Structure

Sumudu P. Leelananda, S. Lindert, 2017 .

Successful Identification of Cardiac Troponin Calcium Sensitizers Using a Combination of Virtual Screening and ROC Analysis of Known Troponin C Binders

Jonathan P. Davis, S. Lindert, Melanie L. Aprahamian, 2017, J. Chem. Inf. Model..

Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling

S. Lindert, Justin T. Seffernick, Zachary C. Drake, 2022, bioRxiv.

Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure.

S. Lindert, Jacob D. Bowman, 2018, The journal of physical chemistry. B.

Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study.

A. McCulloch, S. Lindert, M. Regnier, 2016, The journal of physical chemistry. B.

Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics.

A. McCulloch, J. Mccammon, S. Lindert, 2014, Biophysical journal.

Cryo-Electron Microscopy Structure of an Adenovirus-Integrin Complex Indicates Conformational Changes in both Penton Base and Integrin

P. Stewart, G. Nemerow, M. Silvestry, 2009, Journal of Virology.

Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling.

R. J. Doerksen, J. Prestegard, S. Lindert, 2022, Communications biology.

Effects of HCM cTnI mutation R145G on troponin structure and modulation by PKA phosphorylation elucidated by molecular dynamics simulations.

J. Mccammon, S. Lindert, M. Regnier, 2015, Biophysical journal.

Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder.

S. Lindert, Justin T. Seffernick, Stephanie S. Kim, 2019, The journal of physical chemistry. B.

Hybrid methods for combined experimental and computational determination of protein structure.

S. Lindert, Justin T. Seffernick, 2020, The Journal of chemical physics.

Identification of novel cyclin A2 binding site and nanomolar inhibitors of cyclin A2-CDK2 complex.

S. Lindert, J. Otero, Stephanie S. Kim, 2019, Current computer-aided drug design.

Computational Studies of Cardiac and Skeletal Troponin

S. Lindert, Jacob D. Bowman, 2019, Front. Mol. Biosci..

Applications of machine learning in computer-aided drug discovery

Eric R. Hantz, S. Lindert, Sm Bargeen Alam Turzo, 2022, QRB Discovery.

A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer‐aided Drug Discovery

Meekyum Olivia Kim, J. Mccammon, E. Oldfield, 2015, Chemical biology & drug design.

Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors

Eric R. Hantz, S. Lindert, E. Hantz, 2022, J. Chem. Inf. Model..

Serendipitous Discovery of a Competitive Inhibitor of FraB, a Salmonella Deglycase and Drug Target

S. Lindert, B. Ahmer, V. Wysocki, 2022, Pathogens.

PKA phosphorylation of cardiac troponin I modulates activation and relaxation kinetics of ventricular myofibrils.

A. McCulloch, J. Mccammon, S. Lindert, 2014, Biophysical journal.

Prediction of Intrinsic Disorder Using Rosetta ResidueDisorder and AlphaFold2.

S. Lindert, Justin T. Seffernick, Stephanie S. Kim, 2022, The journal of physical chemistry. B.

Computational Exploration and Characterization of Potential Calcium Sensitizing Mutations in Cardiac Troponin C

S. Lindert, E. Hantz, 2022, J. Chem. Inf. Model..

Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin

S. Lindert, Austin M Cool, 2022, J. Chem. Inf. Model..

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.

Mark J. Mitton-Fry, S. Lindert, C. McElroy, 2021, Journal of medicinal chemistry.

Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus.

S. Lindert, D. Wozniak, Justin T. Seffernick, 2020, ACS medicinal chemistry letters.

Integrated use of biochemical, native mass spectrometry, computational and genome-editing methods to elucidate the mechanism of a Salmonella deglycase.

S. Lindert, B. Ahmer, C. Bell, 2019, Journal of molecular biology.

The effect of magnesium on calcium binding to cardiac troponin C related hypertrophic cardiomyopathy mutants

Eric R. Hantz, S. Lindert, F. van Petegem, 2021, bioRxiv.

Effects of Cardiac Troponin I Mutation P83S on Contractile Properties and the Modulation by PKA-Mediated Phosphorylation.

A. McCulloch, S. Lindert, M. Regnier, 2016, The journal of physical chemistry. B.

Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation*

A. McCulloch, J. Mccammon, S. Lindert, 2015, The Journal of Biological Chemistry.

UDP-galactose 4′-epimerase from the liver fluke, Fasciola hepatica: biochemical characterization of the enzyme and identification of inhibitors

S. Lindert, D. Timson, E. Hoey, 2014, Parasitology.

Comparison of dynamics of wildtype and V94M human UDP-galactose 4-epimerase-A computational perspective on severe epimerase-deficiency galactosemia.

S. Lindert, D. Timson, 2013, Gene.

Computational methods in drug discovery

Sumudu P Leelananda, Steffen Lindert, Sumudu P. Leelananda, 2016, Beilstein journal of organic chemistry.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Cryo-Electron Microscopy Structure of Adenovirus Type 2 Temperature-Sensitive Mutant 1 Reveals Insight into the Cell Entry Defect

Steffen Lindert, Glen R. Nemerow, Phoebe L. Stewart, 2009, Journal of Virology.

Cell-Permeable Bicyclic Peptidyl Inhibitors against NEMO-IκB Kinase Interaction Directly from a Combinatorial Library.

S. Lindert, Qi-En Wang, D. Pei, 2018, Journal of the American Chemical Society.

The Roles of Actin-Binding Domains 1 and 2 in the Calcium-Dependent Regulation of Actin Filament Bundling by Human Plastins.

S. Lindert, E. Kudryashova, D. Kudryashov, 2017, Journal of molecular biology.

Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling

R. J. Doerksen, J. Prestegard, S. Lindert, 2021, Communications Biology.

Antiinfectives targeting enzymes and the proton motive force

J. Mccammon, E. Oldfield, R. Gennis, 2015, Proceedings of the National Academy of Sciences.

Farnesyl Diphosphate Synthase Inhibitors from In Silico Screening

J Andrew McCammon, Steffen Lindert, Wei Zhu, 2013, Chemical biology & drug design.

Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction

S. Lindert, V. Wysocki, J. Prell, 2021, Nature Communications.

Protein Structure Prediction from NMR Hydrogen-Deuterium Exchange Data.

S. Lindert, Justin T. Seffernick, Daniel R. Marzolf, 2021, Journal of chemical theory and computation.

Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs

Jens Meiler, Steffen Lindert, Phoebe L. Stewart, 2013, Comput. Biol. Chem..

Antibacterial drug leads targeting isoprenoid biosynthesis

William Sinko, J Andrew McCammon, Steffen Lindert, 2012, Proceedings of the National Academy of Sciences.

1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition.

S. Lindert, L. Koeth, A. Okumu, 2019, ACS infectious diseases.

Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy.

S. Lindert, V. Wysocki, Sophie R. Harvey, 2021, Analytical chemistry.

Improving inverse docking target identification with Z‐score selection

Steffen Lindert, Stephanie S Kim, Melanie L Aprahamian, 2019, Chemical biology & drug design.

Discovery of Novel Small-Molecule Calcium Sensitizers for Cardiac Troponin C: A Combined Virtual and Experimental Screening Approach

Steffen Lindert, William H Coldren, Svetlana B Tikunova, 2020, J. Chem. Inf. Model..

Binding of calcium and magnesium to human cardiac troponin C

Jonathan P. Davis, S. Lindert, F. van Petegem, 2021, The Journal of biological chemistry.

Binding of Calcium and Magnesium to Cardiac Troponin C

S. Lindert, F. V. Petegem, R. Solaro, 2020, bioRxiv.

Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation.

S. Lindert, V. Wysocki, Yongseok Kim, 2022, Analytical chemistry.

Adaptative Steered Molecular Dynamics Study of Mutagenesis Effects on Calcium Affinity in the Regulatory Domain of Cardiac Troponin C

Steffen Lindert, Eric R. Hantz, S. Lindert, 2021, J. Chem. Inf. Model..

LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders

J Andrew McCammon, Steffen Lindert, Jacob D Durrant, 2012, Chemical biology & drug design.

Umbrella Sampling Simulations of Cardiac Thin Filament Reveal Thermodynamic Consequences of Troponin I Inhibitory Peptide Mutations

S. Lindert, Austin M Cool, 2023, J. Chem. Inf. Model..

Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

J. Andrew McCammon, Steffen Lindert, J. Mccammon, 2015, Journal of chemical theory and computation.

Protein structure prediction using residue-resolved protection factors from hydrogen-deuterium exchange NMR.

Tung T. Nguyen, S. Lindert, Justin T. Seffernick, 2021, Structure.

Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement

Sumudu P Leelananda, Steffen Lindert, Sumudu P. Leelananda, 2019, J. Chem. Inf. Model..

Iterative Molecular Dynamics—Rosetta Protein Structure Refinement Protocol to Improve Model Quality

Jens Meiler, J. Andrew McCammon, Steffen Lindert, 2013, Journal of chemical theory and computation.

Actives-Based Receptor Selection Strongly Increases the Success Rate in Structure-Based Drug Design and Leads to Identification of 22 Potent Cancer Inhibitors

Eric R. Hantz, S. Lindert, E. Hantz, 2022, J. Chem. Inf. Model..

Accounting for Neighboring Residue Hydrophobicity in Diethylpyrocarbonate Labeling Mass Spectrometry Improves Rosetta Protein Structure Prediction.

S. Lindert, R. Vachet, Xiao Pan, 2022, Journal of the American Society for Mass Spectrometry.

Utilization of Hydrophobic Microenvironment Sensitivity in Diethylpyrocarbonate Labeling for Protein Structure Prediction.

S. Lindert, R. Vachet, Patanachai Limpikirati, 2021, Analytical chemistry.

In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors

Steffen Lindert, James Andrew McCammon, Michael D. Burkart, 2014, Journal of Computer-Aided Molecular Design.

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

J. Andrew McCammon, Steffen Lindert, Peter Eastman, 2013, Journal of chemical theory and computation.

Computer‐Aided Drug Discovery Approach Finds Calcium Sensitizer of Cardiac Troponin

J. Mccammon, B. Sykes, S. Lindert, 2015, Chemical biology & drug design.

Dynamics of Plasmodium falciparum enoyl‐ACP reductase and implications on drug discovery

J Andrew McCammon, Steffen Lindert, S. Lindert, 2012, Protein science : a publication of the Protein Society.

Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C+/− During Development

S. Lindert, R. Solaro, P. Lange, 2023, bioRxiv.

Accurate protein structure prediction with hydroxyl radical protein footprinting data

S. Lindert, S. Biehn, 2021, Nature Communications.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

Targeting Troponin C with Small Molecules Containing Diphenyl Moieties: Calcium Sensitivity Effects on Striated Muscles and Structure-Activity Relationship

Jonathan P. Davis, S. Lindert, S. Tikunova, 2023, J. Chem. Inf. Model..

Iterative Molecular Dynamics−Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities

Sumudu P. Leelananda, S. Lindert, 2018 .

Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus.

Mark J. Mitton-Fry, S. Lindert, D. Wozniak, 2020, ACS medicinal chemistry letters.

Antiinfectives targeting enzymes and the proton motive force

E. Oldfield, R. Gennis, S. Lindert, 2015, Proceedings of the National Academy of Sciences.

Cryo-Electron Microscopy Structure of Adenovirus Type 2 Temperature-Sensitive Mutant 1 Reveals Insight into the Cell Entry Defect

P. Stewart, G. Nemerow, M. Silvestry, 2009, Journal of Virology.

Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.

S. Lindert, Sergey Lyskov, Justin T. Seffernick, 2023, Briefings in bioinformatics.

Accurate protein structure prediction with hydroxyl radical protein footprinting data

S. Lindert, S. Biehn, 2021, Nature Communications.

Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application.

S. Lindert, Justin T. Seffernick, Stephanie S. Kim, 2018, The journal of physical chemistry. B.

BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement.

P. Stewart, S. Lindert, J. Meiler, 2011, Journal of structural biology.

Molecular Dynamics and Umbrella Sampling Simulations Elucidate Differences in Troponin C Isoform and Mutant Hydrophobic Patch Exposure.

S. Lindert, Jacob D. Bowman, 2018, The journal of physical chemistry. B.

Relative interfacial cleavage energetics of protein complexes revealed by surface collisions

S. Lindert, V. Wysocki, Andrew S. Norris, 2019, Proceedings of the National Academy of Sciences.

Dynamics and Calcium Association to the N-Terminal Regulatory Domain of Human Cardiac Troponin C: A Multiscale Computational Study

Levi C. T. Pierce, J. Andrew McCammon, Steffen Lindert, 2012, The journal of physical chemistry. B.

Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose‐lysine

S. Lindert, C. Bell, V. Wysocki, 2023, Protein science : a publication of the Protein Society.

Hybrid approaches: applying computational methods in cryo-electron microscopy.

P. Stewart, S. Lindert, J. Meiler, 2009, Current opinion in structural biology.

Structures reveal details of small molecule binding to cardiac troponin.

B. Sykes, S. Lindert, F. West, 2016, Journal of molecular and cellular cardiology.

Iterative Molecular Dynamics—Rosetta Protein Structure Refinement Protocol to Improve Model Quality

S. Lindert, J. Meiler, J. A. McCammon, 2013, Journal of chemical theory and computation.

1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition.

Mark J. Mitton-Fry, S. Lindert, L. Koeth, 2019, ACS infectious diseases.

Discovery of Nanomolar Inhibitors for Human Dihydroorotate Dehydrogenase Using Structure-Based Drug Discovery Methods

S. Lindert, Sandip Vibhute, Chad Bennett, 2024, J. Chem. Inf. Model..

Deep-Learning Structure Elucidation from Single-Mutant Deep Mutational Scanning

S. Lindert, Zachary C. Drake, Elijah Day, 2024, bioRxiv.

Computational studies of the effect of the S23D/S24D troponin I mutation on cardiac troponin structural dynamics.

Rommie E. Amaro, A. McCulloch, S. Lindert, 2014, Biophysical journal.