Tod Romo: search on Z-Library

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1

Insights into the Mechanism of Fengycin, an Antimicrobial Lipopeptide using Multiscale Simulations

Sur, Sreyoshi, Grossfield, Alan, Romo, Tod D.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 37 KB

english, 2016

2

Retinal Makes Concerted Conformational Changes During Early Stages of Rhodopsin Activation

Leioatts, Nicholas, Mertz, Blake, Martínez-Mayorga, Karina, Romo, Tod D., Pitman, Michael C., Feller, Scott E., Grossfield, Alan, Brown, Michael F.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 140 KB

english, 2014

3

Comparision of Membrane Interactions of Acylated and Non-Acylated Lactoferricins by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations

Greathouse, Denise A., Romo, Tod D., Horn, Joshua N., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013

4

A Microsecond Time Scale Molecular Dynamics Simulation of B2AR in a Membrane

Romo, Tod D., Grossfield, Alan, Pitman, Michael C., Deupi, Xavier, Cordomi, Arnau, Kobilka, Brian

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 106 KB

english, 2009

5

Structure-based simulations reveal concerted dynamics of GPCR activation

Leioatts, Nicholas, Suresh, Pooja, Romo, Tod D., Grossfield, Alan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.09 MB

english, 2014

6

Loos: A Tool for Making New Tools for Analyzing Molecular Simulations

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 77 KB

english, 2014

7

Understanding the Effect of Polyunsaturated Fatty Acids on Rhodopsin using All-Atom Molecular Dynamics Simulations

Salas, Letty, Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 42 KB

english, 2016

8

Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics

Joshua N. Horn, Jesse D. Sengillo, Dejun Lin, Tod D. Romo, Alan Grossfield

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

9

Spectral Assignment of Lysozyme Collective Vibrations

Deng, Yanting, Mckinney, Jeffrey, Romo, Tod, Grossfield, Alan, Markelz, Andrea

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 41 KB

english, 2019

10

LOOS: A Suite of Tools to Analyze Molecular Dynamics Simulations

Grossfield, Alan, Romo, Tod D.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 42 KB

2020

11

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Romo, Tod D., Grossfield, Alan, Markelz, Andrea G.

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 2.53 MB

2020

12

Characterization of Chain Order of an Acylated-Lactoferricin Peptide by Solid-State NMR Spectroscopy and All-Atom Molecular Dynamics Simulations

Greathouse, Denise V., Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 101 KB

english, 2011

13

Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations

Tod D. Romo, Laura A. Bradney, Denise V. Greathouse, Alan Grossfield

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2011

Language:

english

File:

PDF, 1.96 MB

english, 2011

14

Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

Romo, Tod D., Leioatts, Nicholas, Grossfield, Alan

Journal:

Journal of Computational Chemistry

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

15

Increase in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State

Deng, Yanting, Luck, Catherine H., Romo, Tod D., Grossfield, Alan M., Bandara, Sepalika, Ren, Zhong, Yang, Xiaojing, Markelz, Andrea G.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

16

Retinal Changes Conformation during the Early Stages of Rhodopsin Activation

Leioatts, Nicholas, Mertz, Blake, Martínez-Mayorga, Karina, Romo, Tod D., Pitman, Michael C., Feller, Scott E., Grossfield, Alan, Brown, Michael F.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013

17

Elucidating Elastic Network Model Robustness by Parametrization with Molecular Dynamics

Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

18

Dynamic Ligand-Protein Interactions Alter Rhodopsin's Conformational Ensemble: Simulations of Rhodopsin and Opsin

Salas, Letty, Leioatts, Nick, Danial, Shairy, Romo, Tod, Grossfield, Alan

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 43 KB

english, 2015

19

Characterization of Rhodopsin's Activation Mechanism using Multi-Basin Structure-Based Models

Salas, Letty, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

20

Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation

Romo, Tod D., Grossfield, Alan

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 910 KB

english, 2011

21

Membrane Interactions of an Acylated and Non-Acylated Lactoferricin Peptide by Solid-State NMR and Fluorescence Spectroscopy and Molecular Dynamics Simulations

Greathouse, Denise A., Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 55 KB

english, 2012

22

Simulating the Mechanism of Antimicrobial Lipopeptides with All-Atom Molecular Dynamics

Horn, Joshua N., Romo, Tod D., Grossfield, Alan

Journal:

Year:

2013

Language:

english

File:

PDF, 407 KB

english, 2013

23

Characterizing the Motion of W6.48 in the Active State of a GPCR

Lynch, Diane, Hurst, Dow, Romo, Tod, Grossfield, Alan, Reggio, Patti, Pitman, Mike

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 117 KB

english, 2012

24

A Sampling Problem in Molecular Dynamics Simulations of Macromolecules

James B. Clarage, Tod Romo, B. Kim Andrews, B. Montgomery Pettitt and George N. Phillips, Jr.

Journal:

Proceedings of the National Academy of Sciences

Year:

1995

Language:

english

File:

PDF, 574 KB

english, 1995

25

Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions

Salas-Estrada, Leslie A., Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 2.10 MB

english, 2018

26

Concerted Motion and Hydration of the Beta-2-Adrenergic Receptor Revealed by Microsecond Time Scale Molecular Dynamics

Romo, Tod D., Grossfield, Alan, Pitman, Michael C.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

27

Elastic Network Models Are Robust to Variations in Formalism

Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 1.30 MB

english, 2012

28

LOOS: A Tool for Making New Tools for Analyzing Molecular Simulations

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 37 KB

english, 2015

29

Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 173 KB

english, 2014

30

Exploring the Mechanisms of Antimicrobial Lipopeptides with Molecular Simulation

Grossfield, Alan, Horn, Joshua N., Romo, Tod D., Lin, Dejun, Cravens, Aaron

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 49 KB

english, 2013

31

How Fast is Your Camera? Timescales for Molecular Motion and their Role in Restraining Molecular Dynamics

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 144 KB

english, 2014

32

Selectivity and Mechanism of Fengycin, an Antimicrobial Lipopeptide from Molecular Dynamics

Sur, Sreyoshi, Romo, Tod D, Grossfield, Alan

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.66 MB

english, 2018

33

Validating and improving elastic network models with molecular dynamics simulations

Tod D. Romo, Alan Grossfield

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 536 KB

english, 2011

34

Binding of Antimicrobial Lipopeptides To Lipid Bilayers Characterized By Microsecond Molecular Dynamics Simulations

Horn, Joshua N., Romo, Tod D., Pitman, Michael C., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 70 KB

english, 2010

35

Characterization of Membrane Interactions with Lactoferricin Peptides by Both All-Atom and Coarse-Grained Molecular Dynamics Simulations, Solid-State NMR, and Fluorescence Spectroscopy

Romo, Tod D., Horn, Joshua, Greathouse, Denise V., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

36

Validating and Improving Elastic Network Models Using Molecular Dynamics

Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

37

Lactoferricin Peptides Characterized Using All-Atom Molecular Dynamics Simulations and Solid State NMR

Romo, Tod, Greathouse, Denise V., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 71 KB

english, 2011

38

Unraveling Allostery with Simulations of Rhodopsin Photocycle Intermediates

Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 36 KB

english, 2013

39

Loos: A Toolkit for Analyzing Molecular Simulations and Making New Tools

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

40

Loos: A Tool for Making New Tools for Analyzing Molecular Simulations

Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 34 KB

english, 2013

41

DETERMINING RELEVANT FEATURES TO RECOGNIZE ELECTRON DENSITY PATTERNS IN X-RAY PROTEIN CRYSTALLOGRAPHY

GOPAL, KRESHNA, ROMO, TOD D., SACCHETTINI, JAMES C., IOERGER, THOMAS R.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2005

Language:

english

File:

PDF, 691 KB

english, 2005

42

Minimal Nucleation State of α-Synuclein Is Stabilized by Dynamic Threonine–Water Networks

Romo, Tod D., Lewis, Andrew K., Braun, Anthony R., Grossfield, Alan, Sachs, Jonathan N.

Journal:

ACS Chemical Neuroscience

Year:

2017

Language:

english

File:

PDF, 1.17 MB

english, 2017

43

Loos: A Tool for Making Tools to Analyze Molecular Dynamics Simulations

Grossfield, Alan, Romo, Tod D.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 43 KB

english, 2019

44

Retinal Ligand Mobility Explains Internal Hydration and Reconciles Active Rhodopsin Structures

Leioatts, Nicholas, Mertz, Blake, Martínez-Mayorga, Karina, Romo, Tod D., Pitman, Michael C., Feller, Scott E., Grossfield, Alan, Brown, Michael F.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.58 MB

english, 2014

45

Erratum

Romo, Tod D., Grossfield, Alan

Journal:

Pediatric Neurology

Year:

1987

Language:

english

File:

PDF, 34 KB

english, 1987

46

Computational Studies of Alpha-Synuclein Fibril Formation and Stability

Beaven, Andrew H., Romo, Tod D., Lewis, Andrew K., Braun, Anthony R., Grossfield, Alan, Sachs, Jonathan N.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

47

Acylated Lactoferrin Peptides Using Solid State NMR and All-Atom Molecular Dynamics Simulations

Romo, Tod D., Grossfield, Alan, Bradney, Laura, Greathouse, Denise V.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 38 KB

english, 2010

48

Protein-Assisted Pericyclic Reactions: An Alternate Hypothesis for the Action of Quantal Receptors

Radding, Wilson, Romo, Tod, Phillips, George N.

Journal:

Biophysical Journal

Year:

1999

Language:

english

File:

PDF, 904 KB

english, 1999

49

All-Atom Simulations Reveal Ensemble Dynamics of Rhodopsin

Leioatts, Nicholas, Romo, Tod D., Grossfield, Alan

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 39 KB

english, 2014

50

Characterizing global substates of myoglobin

B Kim Andrews, Tod Romo, James B Clarage, B Montgomery Pettitt, George N Phillips Jr

Journal:

Year:

1998

Language:

english

File:

PDF, 683 KB

english, 1998

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