Steffen, Lindert: search on Z-Library

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1

Computational methods in drug discovery

Leelananda, Sumudu P, Lindert, Steffen

Journal:

Beilstein Journal of Organic Chemistry

Year:

2016

Language:

english

File:

PDF, 3.47 MB

english, 2016

2

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

Lindert, Steffen, Kekenes-Huskey, Peter M., Huber, Gary, Pierce, Levi, McCammon, J. Andrew

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 5.13 MB

english, 2012

3

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

Leelananda, Sumudu P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 4.82 MB

english, 2019

4

Differences in Troponin C Dynamics Between Cardiac and Skeletal Muscle - A Molecular Dynamics Perspective

Lindert, Steffen, McCammon, Andy

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

5

Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors

Kim, Stephanie, Alves, Michele, Gygli, Patrick, Otero, Jose, Lindert, Steffen

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 42 KB

english, 2019

6

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

Coldren, William H., Tikunova, Svetlana B., Davis, Jonathan P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 3.60 MB

2020

7

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

Lu, Yanran, Papa, Jonathan L., Nolan, Sheri, English, Anthony, Seffernick, Justin T., Shkolnikov, Nicholas, Powell, Josh, Lindert, Steffen, Wozniak, Daniel J., Yalowich, Jack, Mitton-Fry, Mark J.

Journal:

ACS Medicinal Chemistry Letters

Year:

2020

File:

PDF, 3.75 MB

2020

8

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

Aprahamian, Melanie L., Chea, Emily E., Jones, Lisa M., Lindert, Steffen

Journal:

Analytical Chemistry

Year:

2018

Language:

english

File:

PDF, 1.84 MB

english, 2018

9

Farnesyl Diphosphate Synthase Inhibitors from In Silico Screening

Lindert, Steffen, Zhu, Wei, Liu, Yi-Liang, Pang, Ran, Oldfield, Eric, McCammon, J. Andrew

Journal:

Chemical Biology & Drug Design

Year:

2013

Language:

english

File:

PDF, 596 KB

english, 2013

10

Exploring How Phosphorylation Influences C-I Interaction and Calcium Sensitivity of Troponin by Molecular Dynamics Simulations

Cheng, Yuanhua, Lindert, Steffen, Kekenes-Huskey, Peter, Rao, Vijay S., Rosevear, Paul R., McCammon, J. Andrew, McCulloch, Andrew, Regnier, Michael

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 49 KB

english, 2014

11

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

Cheng, Yuanhua, Lindert, Steffen, Oxenford, Lucas, Tu, An-yue, McCulloch, Andrew D., Regnier, Michael

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 8.70 MB

english, 2016

12

Molecular Effects of Cardiac Troponin DCM Mutations on Calcium Sensitivity and Myofilament Activation - an Integrated Multi-Scale Modeling Study

Dewan, Sukriti, McCabe, Kimberly, Regnier, Michael, McCulloch, Andrew, Lindert, Steffen

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

13

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

Lindert, Steffen, Stewart, Phoebe L., Meiler, Jens

Journal:

Computational Biology and Chemistry

Year:

2013

Language:

english

File:

PDF, 676 KB

english, 2013

14

Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields

Götz, Andreas W., Bucher, Denis, Lindert, Steffen, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.78 MB

english, 2014

15

Long-Timescale Molecular Dynamics Simulations Elucidate the Dynamics and Kinetics of Exposure of the Hydrophobic Patch in Troponin C

Lindert, Steffen, Kekenes-Huskey, Peter M., McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 568 KB

english, 2012

16

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

Feixas, Ferran, Lindert, Steffen, Sinko, William, McCammon, J. Andrew

Journal:

Biophysical Chemistry

Year:

2014

Language:

english

File:

PDF, 1.22 MB

english, 2014

17

RESECTION OF THE ELBOW IN THREE CASES.

Lindert, Steffen, Stewart, Phoebe L., Meiler, Jens

Journal:

Year:

1857

Language:

english

File:

PDF, 224 KB

english, 1857

18

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

Aprahamian, Melanie L., Lindert, Steffen

Journal:

Journal of Chemical Theory and Computation

Year:

2019

File:

PDF, 3.60 MB

2019

19

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

Steffen Lindert, Tommy Hofmann, Nils Wötzel, Mert Karakaş, Phoebe L. Stewart, Jens Meiler

Journal:

Year:

2012

Language:

english

File:

PDF, 1.33 MB

english, 2012

20

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

Lindert, Steffen, Maslennikov, Innokentiy, Chiu, Ellis J.C., Pierce, Levi C., McCammon, J. Andrew, Choe, Senyon

Journal:

Biochemical and Biophysical Research Communications

Year:

2014

Language:

english

File:

PDF, 3.10 MB

english, 2014

21

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

Lindert, Steffen, Li, Monica X., Sykes, Brian D., McCammon, J. Andrew

Journal:

Chemical Biology & Drug Design

Year:

2015

Language:

english

File:

PDF, 998 KB

english, 2015

22

Designing a High Affinity Cardiac Troponin Activator

Cai, Fangze, Li, Monica, Pineda-Sanabria, Sandra, Gelozia, Shorena, Lindert, Steffen, McCammon, J. Andrew, West, Frederick, Sykes, Brian, Hwang, Peter

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 46 KB

english, 2016

23

EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps

Steffen Lindert, Nathan Alexander, Nils Wötzel, Mert Karakaş, Phoebe L. Stewart, Jens Meiler

Journal:

Year:

2012

Language:

english

File:

PDF, 2.29 MB

english, 2012

24

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

Lindert, Steffen, Bucher, Denis, Eastman, Peter, Pande, Vijay, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.82 MB

english, 2013

25

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

Dewan, Sukriti, McCabe, Kimberly J., Regnier, Michael, McCulloch, Andrew D., Lindert, Steffen

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 3.06 MB

english, 2016

26

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

Leelananda, Sumudu, Lindert, Steffen

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

27

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

Steffen Lindert, Jacob D. Durrant, J. Andrew McCammon

Journal:

Chemical Biology & Drug Design

Year:

2012

Language:

english

File:

PDF, 400 KB

english, 2012

28

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

Aprahamian, Melanie L., Lindert, Steffen

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 3.60 MB

english, 2019

29

Relative interfacial cleavage energetics of protein complexes revealed by surface collisions

Harvey, Sophie R., Seffernick, Justin T., Quintyn, Royston S., Song, Yang, Ju, Yue, Yan, Jing, Sahasrabuddhe, Aniruddha N., Norris, Andrew, Zhou, Mowei, Behrman, Edward J., Lindert, Steffen, Wysocki,

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 889 KB

english, 2019

30

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

Lindert, Steffen, McCammon, J. Andrew

Journal:

Protein Science

Year:

2012

Language:

english

File:

PDF, 1.50 MB

english, 2012

31

Relative interfacial cleavage energetics of protein complexes revealed by surface collisions

Harvey, Sophie R., Seffernick, Justin T., Quintyn, Royston S., Song, Yang, Ju, Yue, Yan, Jing, Sahasrabuddhe, Aniruddha N., Norris, Andrew, Zhou, Mowei, Behrman, Edward J., Lindert, Steffen, Wysocki,

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

File:

PDF, 889 KB

2019

32

Hybrid approaches: applying computational methods in cryo-electron microscopy

Steffen Lindert, Phoebe L Stewart, Jens Meiler

Journal:

Current Opinion in Structural Biology

Year:

2009

Language:

english

File:

PDF, 3.26 MB

english, 2009

33

Mechanisms of Altered Cardiac Myofibril Relaxation Caused by the Cardiac Troponin-I R145G Mutation

Rao, Vijay S., Lindert, Steffen, Wang, Dan D., Kekenes-Huskey, Peter, Cheng, Yuanhua, McCammon, J. Andrew, McCulloch, Andrew, Arzberger, Peter, Regnier, Michael

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 38 KB

english, 2013

34

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

Smith, Jason G., Silvestry, Mariena, Lindert, Steffen, Lu, Wuyuan, Nemerow, Glen R., Stewart, Phoebe L., Sherry, Barbara

Journal:

Year:

2010

Language:

english

File:

PDF, 746 KB

english, 2010

35

Antiinfectives targeting enzymes and the proton motive force

Feng, Xinxin, Zhu, Wei, Schurig-Briccio, Lici A., Lindert, Steffen, Shoen, Carolyn, Hitchings, Reese, Li, Jikun, Wang, Yang, Baig, Noman, Zhou, Tianhui, Kim, Boo Kyung, Crick, Dean C., Cynamon, Michae

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 2.28 MB

english, 2015

36

PKA Phosphorylation of Cardiac Troponin I Modulates Activation and Relaxation Kinetics of Ventricular Myofibrils

Rao, Vijay, Cheng, Yuanhua, Lindert, Steffen, Wang, Dan, Oxenford, Lucas, McCulloch, Andrew D., McCammon, J. Andrew, Regnier, Michael

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 728 KB

english, 2014

37

In silicoscreening forPlasmodium falciparumenoyl-ACP reductase inhibitors

Lindert, Steffen, Tallorin, Lorillee, Nguyen, Quynh G., Burkart, Michael D., McCammon, J. Andrew

Journal:

Journal of Computer-Aided Molecular Design

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

38

Structures reveal details of small molecule binding to cardiac troponin

Cai, Fangze, Li, Monica X., Pineda-Sanabria, Sandra E., Gelozia, Shorena, Lindert, Steffen, West, Frederick, Sykes, Brian D., Hwang, Peter M.

Journal:

Journal of Molecular and Cellular Cardiology

Year:

2016

Language:

english

File:

PDF, 3.81 MB

english, 2016

39

Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application

Kim, Stephanie S., Seffernick, Justin T., Lindert, Steffen

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.42 MB

english, 2018

40

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

Leelananda, Sumudu P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 4.82 MB

2019

41

Cryo-EM Guided de novo Protein Fold Elucidation

Lindert, Steffen, Staritzbichler, Rene, Woetzel, Nils, Karakas, Mert, Stewart, Phoebe, Meiler, Jens

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 36 KB

english, 2009

42

Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation Elucidated by Molecular Dynamics Simulations

Lindert, Steffen, Cheng, Yuanhua, Kekenes-Huskey, Peter, Regnier, Michael, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 2.80 MB

english, 2015

43

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

ZINSSER, VERONIKA L., LINDERT, STEFFEN, BANFORD, SAMANTHA, HOEY, ELIZABETH M., TRUDGETT, ALAN, TIMSON, DAVID J.

Journal:

Year:

2015

Language:

english

File:

PDF, 522 KB

english, 2015

44

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

Aprahamian, Melanie L., Tikunova, Svetlana B., Price, Morgan V., Cuesta, Andres F., Davis, Jonathan P., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 3.08 MB

english, 2017

45

Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations

Bowman, Jacob D., Coldren, William H., Lindert, Steffen

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 2.80 MB

english, 2019

46

Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a deglycase

Sengupta, Anindita, Wu, Jikang, Seffernick, Justin T., Sabag-Daigle, Anice, Thomsen, Nicholas, Chen, Tien-Hao, Capua, Angela Di, Bell, Charles E., Ahmer, Brian M.M., Lindert, Steffen, Wysocki, Vicki H

Journal:

Journal of Molecular Biology

Year:

2019

Language:

english

File:

PDF, 2.11 MB

english, 2019

47

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

Lindert, Steffen, Meiler, Jens, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 3.34 MB

english, 2013

48

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

Bowman, Jacob D., Lindert, Steffen

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.30 MB

english, 2018

49

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

Aprahamian, Melanie, Tikunova, Svetlana, Davis, Jonathan, Lindert, Steffen

Journal:

Journal of Molecular and Cellular Cardiology

Year:

2018

File:

PDF, 46 KB

2018

50

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

Nils Woetzel, Steffen Lindert, Phoebe L. Stewart, Jens Meiler

Journal:

Journal of Structural Biology

Year:

2011

Language:

english

File:

PDF, 1.44 MB

english, 2011

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