Gumbart, James C. : rechercher sur Z-Library

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1

Scalable molecular dynamics with NAMD

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten

Journal:

Journal of Computational Chemistry

Année:

2005

Langue:

english

Fichier:

PDF, 977 KB

english, 2005

2

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

Comer, Jeffrey, Gumbart, James C., Hénin, Jérôme, Lelièvre, Tony, Pohorille, Andrew, Chipot, Christophe

Journal:

Journal of Physical Chemistry B

Année:

2015

Langue:

english

Fichier:

PDF, 3.10 MB

english, 2015

3

Resolving the Mechanisms of Bacterial Resistance to Macrolide Antibiotics

Pavlova, Anna, Gumbart, James C.

Journal:

Biophysical Journal

Année:

2015

Langue:

english

Fichier:

PDF, 38 KB

english, 2015

4

Rapid parameterization of small molecules using the force field toolkit

Mayne, Christopher G., Saam, Jan, Schulten, Klaus, Tajkhorshid, Emad, Gumbart, James C.

Journal:

Journal of Computational Chemistry

Année:

2013

Langue:

english

Fichier:

PDF, 1.12 MB

english, 2013

5

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD

Jiang, Wei, Phillips, James C., Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., Luo, Yun, Schulten, Klaus, Roux, Benoît

Journal:

Computer Physics Communications

Année:

2014

Langue:

english

Fichier:

PDF, 1.49 MB

english, 2014

6

Resolving the Mechanisms of Bacterial Resistance to Macrolide Antibiotics

Pavlova, Anna, Gumbart, James C.

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 43 KB

english, 2014

7

Parametrization of macrolide antibiotics using the force field toolkit

Pavlova, Anna, Gumbart, James C

Journal:

Journal of Computational Chemistry

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

8

Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation

Hwang, Hyea, McCaslin, Tyler G., Hazel, Anthony, Pagba, Cynthia V., Nevin, Christina M., Pavlova, Anna, Barry, Bridgette A., Gumbart, James C.

Journal:

Journal of Physical Chemistry B

Année:

2017

Langue:

english

Fichier:

PDF, 3.14 MB

english, 2017

9

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-energy Calculations

Fu, Haohao, Gumbart, James C., Chen, Haochuan, Shao, Xueguang, Cai, Wensheng, Chipot, Christophe

Journal:

Journal of Chemical Information and Modeling

Année:

2018

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2018

10

Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA

Darzynkiewicz, Zbigniew M., Green, Adam T., Abdali, Narges, Hazel, Anthony, Fulton, Ronnie L., Kimball, Joseph, Gryczynski, Zygmunt, Gumbart, James C., Parks, Jerry M., Smith, Jeremy C., Zgurskaya, He

Journal:

Biophysical Journal

Année:

2019

Langue:

english

Fichier:

PDF, 1.78 MB

english, 2019

11

Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette

McCaslin, Tyler G., Pagba, Cynthia V., Hwang, Hyea, Gumbart, James C., Chi, San-Hui, Perry, Joseph W., Barry, Bridgette A.

Journal:

Chemical Communications

Année:

2019

Langue:

english

Fichier:

PDF, 2.10 MB

english, 2019

12

Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette

McCaslin, Tyler G., Pagba, Cynthia V., Hwang, Hyea, Gumbart, James C., Chi, San-Hui, Perry, Joseph W., Barry, Bridgette A.

Journal:

Chemical Communications

Année:

2019

Fichier:

PDF, 2.10 MB

2019

13

Fatal arrhythmias: Another reason why doctors remain cautious about chloroquine/hydroxychloroquine for treating COVID-19

Uzelac, Ilija, Iravanian, Shahriar, Ashikaga, Hiroshi, Bhatia, Neal K., Herndon, Conner, Kaboudian, Abouzar, Gumbart, James C., Cherry, Elizabeth M., Fenton, Flavio H.

Journal:

Année:

2020

Fichier:

PDF, 2.62 MB

2020

14

Self-Assembly of Photosynthetic Membranes

Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, Klaus Schulten

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 732 KB

english, 2010

15

Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

Frauenfeld, Jens, Gumbart, James, Sluis, Eli O van der, Funes, Soledad, Gartmann, Marco, Beatrix, Birgitta, Mielke, Thorsten, Berninghausen, Otto, Becker, Thomas, Schulten, Klaus

Journal:

Nature Structural and Molecular Biology

Année:

2011

Langue:

english

Fichier:

PDF, 3.75 MB

english, 2011

16

Molecular dynamics simulations of proteins in lipid bilayers

James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, Klaus Schulten

Journal:

Current Opinion in Structural Biology

Année:

2005

Langue:

english

Fichier:

PDF, 304 KB

english, 2005

17

Molecular dynamics simulations of membrane channels and transporters

Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, Klaus Schulten

Journal:

Current Opinion in Structural Biology

Année:

2009

Langue:

english

Fichier:

PDF, 2.63 MB

english, 2009

18

Regulation of the Protein-Conducting Channel by a Bound Ribosome

James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, Klaus Schulten

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 2.52 MB

english, 2009

19

Symmetry-Restrained Flexible Fitting for Symmetric EM Maps

Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, Klaus Schulten

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2011

20

Constant electric field simulations of the membrane potential illustrated with simple systems

James Gumbart, Fatemeh Khalili-Araghi, Marcos Sotomayor, Benoît Roux

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Année:

2012

Langue:

english

Fichier:

PDF, 2.04 MB

english, 2012

21

Coupling of Calcium and Substrate Binding through Loop Alignment in the Outer-Membrane Transporter BtuB

James Gumbart, Michael C. Wiener, Emad Tajkhorshid

Journal:

Journal of Molecular Biology

Année:

2009

Langue:

english

Fichier:

PDF, 2.22 MB

english, 2009

22

Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter

Travis J. Barnard, James Gumbart, Janine H. Peterson, Nicholas Noinaj, Nicole C. Easley, Nathalie Dautin, Adam J. Kuszak, Emad Tajkhorshid, Harris D. Bernstein, Susan K. Buchanan

Journal:

Journal of Molecular Biology

Année:

2012

Langue:

english

Fichier:

PDF, 1.75 MB

english, 2012

23

Applications of the molecular dynamics flexible fitting method

Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth Villa, Klaus Schulten

Journal:

Journal of Structural Biology

Année:

2011

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2011

24

Regulation of the Protein-conducting Channel by a Bound Ribosome

Gumbart, James C., Trabuco, Leonardo G., Villa, Elizabeth, Schreiner, Eduard, Harrison, Christopher B., Schulten, Klaus

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 38 KB

english, 2009

25

Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting

Hsin, Jen, Gumbart, James, Trabuco, Leonardo G., Villa, Elizabeth, Qian, Pu, Hunter, C. Neil, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2009

26

Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s

Chandler, Danielle E., Gumbart, James, Stack, John D., Chipot, Christophe, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 595 KB

english, 2009

27

Recent Developments of the Molecular Dynamics Flexible Fitting Method

Chan, Kwok Yan, Trabuco, Leonardo G., Gumbart, James, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2010

Langue:

english

Fichier:

PDF, 56 KB

english, 2010

28

Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

Gumbart, James, Roux, Benoît

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 598 KB

english, 2012

29

Mechanisms of SecM-Mediated Stalling in the Ribosome

Gumbart, James, Schreiner, Eduard, Wilson, Daniel N., Beckmann, Roland, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 919 KB

english, 2012

30

A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism

Broadley, Simon Gareth, Gumbart, James Conrad, Weber, Brandon William, Marakalala, Mohlopheni Jackson, Steenkamp, Daniel Jacobus, Sewell, Bryan Trevor

Journal:

Acta Crystallographica Section D Biological Crystallography

Année:

2012

Langue:

english

Fichier:

PDF, 1.73 MB

english, 2012

31

Molecular Dynamics Studies of the Archaeal Translocon

Gumbart, James, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2006

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2006

32

Mechanics of Force Propagation in TonB-Dependent Outer Membrane Transport

Gumbart, James, Wiener, Michael C., Tajkhorshid, Emad

Journal:

Biophysical Journal

Année:

2007

Langue:

english

Fichier:

PDF, 1.07 MB

english, 2007

33

Intrinsic Curvature Properties of Photosynthetic Proteins in Chromatophores

Chandler, Danielle E., Hsin, Jen, Harrison, Christopher B., Gumbart, James, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2008

Langue:

english

Fichier:

PDF, 3.58 MB

english, 2008

34

Architecture and assembly of the Gram-positive cell wall

Beeby, Morgan, Gumbart, James C., Roux, Benoît, Jensen, Grant J.

Journal:

Molecular Microbiology

Année:

2013

Langue:

english

Fichier:

PDF, 786 KB

english, 2013

35

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

Gumbart, James C., Roux, Benoît, Chipot, Christophe

Journal:

Journal of Chemical Theory and Computation

Année:

2013

Langue:

english

Fichier:

PDF, 958 KB

english, 2013

36

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

Gumbart, James C., Roux, Benoît, Chipot, Christophe

Journal:

Journal of Chemical Theory and Computation

Année:

2013

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2013

37

Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane–Protein Insertion

Gumbart, James C., Teo, Ivan, Roux, Benoît, Schulten, Klaus

Journal:

Journal of the American Chemical Society

Année:

2013

Langue:

english

Fichier:

PDF, 433 KB

english, 2013

38

Structural insight into the biogenesis of β-barrel membrane proteins

Noinaj, Nicholas, Kuszak, Adam J., Gumbart, James C., Lukacik, Petra, Chang, Hoshing, Easley, Nicole C., Lithgow, Trevor, Buchanan, Susan K.

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.86 MB

english, 2013

39

IcmQ in the Type 4b Secretion System Contains an NAD+ Binding Domain

Farelli, Jeremiah D., Gumbart, James C., Akey, Ildikó V., Hempstead, Andrew, Amyot, Whitney, Head, James F., McKnight, C. James, Isberg, Ralph R., Akey, Christopher W.

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 3.42 MB

english, 2013

40

[ACM Press the 1st Conference of the Extreme Science and Engineering Discovery Environment - Chicago, Illinois (2012.07.16-2012.07.20)] Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment on Bridging from the eXtreme to the campus and beyond - XSEDE '12 - Membrane protein simulations under asymmetric ionic concentrations

Khalili-Araghi, Fatemeh, Ziervogel, Brigitte, Roux, Benoît, Gumbart, James

Année:

2012

Langue:

english

Fichier:

PDF, 102 KB

english, 2012

41

The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state

Briegel, Ariane, Ames, Peter, Gumbart, James C., Oikonomou, Catherine M., Parkinson, John S., Jensen, Grant J.

Journal:

Molecular Microbiology

Année:

2013

Langue:

english

Fichier:

PDF, 1003 KB

english, 2013

42

Structure of the SecY channel during initiation of protein translocation

Park, Eunyong, Ménétret, Jean-François, Gumbart, James C., Ludtke, Steven J., Li, Weikai, Whynot, Andrew, Rapoport, Tom A., Akey, Christopher W.

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2013

43

Thermodynamics of Deca-alanine Folding in Water

Hazel, Anthony, Chipot, Christophe, Gumbart, James C.

Journal:

Journal of Chemical Theory and Computation

Année:

2014

Langue:

english

Fichier:

PDF, 2.69 MB

english, 2014

44

Mechanisms of Membrane-Protein Insertion at the Inner and Outer Membranes

Gumbart, James C.

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 46 KB

english, 2014

45

Protein Folding and Membrane Insertion via the Protein Translocon

Gumbart, James C., Chipot, Christophe, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2011

Langue:

english

Fichier:

PDF, 35 KB

english, 2011

46

Assembly and Architecture of Gram-Positive and -Negative Cell Walls

Gumbart, James C., Beeby, Morgan, Jensen, Grant, Roux, Benoit

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 37 KB

english, 2013

47

Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane-Protein Insertion

Gumbart, James C., Teo, Ivan, Roux, Benoit, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 37 KB

english, 2013

48

ESTRO meetings

Jiang, Wei, Phillips, James C., Huang, Lei, Fajer, Mikolai, Meng, Yilin, Gumbart, James C., Luo, Yun, Schulten, Klaus, Roux, Benoît

Journal:

Radiotherapy and Oncology

Année:

1996

Langue:

english

Fichier:

PDF, 41 KB

english, 1996

49

Coupling of Ca2+ and Substrate Binding in the Outer Membrane Transporter BtuB

Gumbart, James C., Wiener, Michael C., Tajkhorshid, Emad

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 98 KB

english, 2009

50

Spontaneous Movement of Transmembrane Segments from SecY into the Membrane

Gumbart, James C., Roux, Benoit, Schulten, Klaus

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 64 KB

english, 2012