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Title: Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

Abstract

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describemore » how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.« less

Authors:
ORCiD logo [1];  [2]; ORCiD logo [2];  [3];  [3]; ORCiD logo [4]; ORCiD logo [2];  [1]; ORCiD logo [1];  [3];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [2];  [3];  [3];  [3]; ORCiD logo [3];  [2] more »;  [3];  [3];  [2]; ORCiD logo [1];  [2]; ORCiD logo [1] « less
+ Show Author Affiliations
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  2. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  3. Frederick National Lab. for Cancer Research, Frederick, MD (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Frederick National Lab. for Cancer Research, Frederick, MD (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA); National Cancer Institute (NCI); USDOE Office of Science (SC)
OSTI Identifier:
1885350
Alternate Identifier(s):
OSTI ID: 1894845; OSTI ID: 2204111
Report Number(s):
LLNL-JRNL-830356; LA-UR-22-20618; LLNL-JRNL-855692
Journal ID: ISSN 1549-9618
Grant/Contract Number:  
AC05-00OR22725; AC52-07NA27344; AC52-06NA25396; HHSN261200800001E; 89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 18; Journal Issue: 8; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Lopez Bautista, Cesar Augusto, Zhang, Xiaohua, Aydin, Fikret, Shrestha, Rebika, Van, Que N., Stanley, Christopher B., Carpenter, Timothy S., Nguyen, Kien, Patel, Lara Anne, Chen, De, Burns, Violetta, Hengartner, Nicolas W., Reddy, Tyler John Edward, Bhatia, Harsh, Di Natale, Francesco, Tran, Timothy H., Chan, Albert H., Simanshu, Dhirendra K., Nissley, Dwight V., Streitz, Frederick H., Stephen, Andrew G., Turbyville, Thomas J., Lightstone, Felice C., Gnanakaran, Sandrasegaram, Ingolfsson, Helgi I., and Neale, Christopher Andrew. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. United States: N. p., 2022. Web. doi:10.1021/acs.jctc.2c00168.
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Lopez Bautista, Cesar Augusto, Zhang, Xiaohua, Aydin, Fikret, Shrestha, Rebika, Van, Que N., Stanley, Christopher B., Carpenter, Timothy S., Nguyen, Kien, Patel, Lara Anne, Chen, De, Burns, Violetta, Hengartner, Nicolas W., Reddy, Tyler John Edward, Bhatia, Harsh, Di Natale, Francesco, Tran, Timothy H., Chan, Albert H., Simanshu, Dhirendra K., Nissley, Dwight V., Streitz, Frederick H., Stephen, Andrew G., Turbyville, Thomas J., Lightstone, Felice C., Gnanakaran, Sandrasegaram, Ingolfsson, Helgi I., & Neale, Christopher Andrew. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework. United States. https://doi.org/10.1021/acs.jctc.2c00168
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Lopez Bautista, Cesar Augusto, Zhang, Xiaohua, Aydin, Fikret, Shrestha, Rebika, Van, Que N., Stanley, Christopher B., Carpenter, Timothy S., Nguyen, Kien, Patel, Lara Anne, Chen, De, Burns, Violetta, Hengartner, Nicolas W., Reddy, Tyler John Edward, Bhatia, Harsh, Di Natale, Francesco, Tran, Timothy H., Chan, Albert H., Simanshu, Dhirendra K., Nissley, Dwight V., Streitz, Frederick H., Stephen, Andrew G., Turbyville, Thomas J., Lightstone, Felice C., Gnanakaran, Sandrasegaram, Ingolfsson, Helgi I., and Neale, Christopher Andrew. Fri . "Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework". United States. https://doi.org/10.1021/acs.jctc.2c00168. https://www.osti.gov/servlets/purl/1885350.
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@article{osti_1885350,
title = {Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework},
author = {Lopez Bautista, Cesar Augusto and Zhang, Xiaohua and Aydin, Fikret and Shrestha, Rebika and Van, Que N. and Stanley, Christopher B. and Carpenter, Timothy S. and Nguyen, Kien and Patel, Lara Anne and Chen, De and Burns, Violetta and Hengartner, Nicolas W. and Reddy, Tyler John Edward and Bhatia, Harsh and Di Natale, Francesco and Tran, Timothy H. and Chan, Albert H. and Simanshu, Dhirendra K. and Nissley, Dwight V. and Streitz, Frederick H. and Stephen, Andrew G. and Turbyville, Thomas J. and Lightstone, Felice C. and Gnanakaran, Sandrasegaram and Ingolfsson, Helgi I. and Neale, Christopher Andrew},
abstractNote = {The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.},
doi = {10.1021/acs.jctc.2c00168},
journal = {Journal of Chemical Theory and Computation},
number = 8,
volume = 18,
place = {United States},
year = {Fri Jul 22 00:00:00 EDT 2022},
month = {Fri Jul 22 00:00:00 EDT 2022}
}
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Works referenced in this record:

Recapitulation of cell-like KRAS4b membrane dynamics on complex biomimetic membranes
journal, January 2022

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
journal, February 2013

  • Le Grand, Scott; Götz, Andreas W.; Walker, Ross C.
  • Computer Physics Communications, Vol. 184, Issue 2
  • DOI: 10.1016/j.cpc.2012.09.022

Multiscale Coarse-Graining of Monosaccharides
journal, October 2007

  • Liu, Pu; Izvekov, Sergei; Voth, Gregory. A.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 39
  • DOI: 10.1021/jp0721494

Dual Resolution Membrane Simulations Using Virtual Sites
journal, April 2020

  • Liu, Yang; De Vries, Alex H.; Barnoud, Jonathan
  • The Journal of Physical Chemistry B, Vol. 124, Issue 19
  • DOI: 10.1021/acs.jpcb.0c01842

Systematic multiscale simulation of membrane protein systems
journal, April 2009

Analysis of a DNA simulation model through hairpin melting experiments
journal, September 2010

  • Linak, Margaret C.; Dorfman, Kevin D.
  • The Journal of Chemical Physics, Vol. 133, Issue 12
  • DOI: 10.1063/1.3480685

Pitfalls of the Martini Model
journal, September 2019

  • Alessandri, Riccardo; Souza, Paulo C. T.; Thallmair, Sebastian
  • Journal of Chemical Theory and Computation, Vol. 15, Issue 10
  • DOI: 10.1021/acs.jctc.9b00473

Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models
journal, January 2011

  • Paschek, Dietmar; Day, Ryan; García, Angel E.
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 44
  • DOI: 10.1039/c1cp22110h

Conservation of cis prolyl bonds in proteins during evolution
journal, December 2004

  • Lorenzen, Stephan; Peters, Björn; Goede, Andrean
  • Proteins: Structure, Function, and Bioinformatics, Vol. 58, Issue 3
  • DOI: 10.1002/prot.20342

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
journal, July 2016

  • Zavadlav, J.; Podgornik, R.; Melo, M. N.
  • The European Physical Journal Special Topics, Vol. 225, Issue 8-9
  • DOI: 10.1140/epjst/e2016-60117-8

Conformational Transitions in p21 ras and in Its Complexes with the Effector Protein Raf-RBD and the GTPase Activating Protein GAP †
journal, January 1996

  • Geyer, Matthias; Schweins, Thomas; Herrmann, Christian
  • Biochemistry, Vol. 35, Issue 32
  • DOI: 10.1021/bi952858k

Direct Simulation of Protein-Mediated Vesicle Fusion: Lung Surfactant Protein B
journal, October 2010

Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study
journal, May 2015

  • Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Li, Hung-Sheng
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1848, Issue 5
  • DOI: 10.1016/j.bbamem.2015.02.016

Non-proline Cis peptide bonds in proteins
journal, February 1999

  • Jabs, Andreas; Weiss, Manfred S.; Hilgenfeld, Rolf
  • Journal of Molecular Biology, Vol. 286, Issue 1
  • DOI: 10.1006/jmbi.1998.2459

Exploring CRD mobility during RAS/RAF engagement at the membrane
journal, July 2022

Dynamic density functional theory of fluids
journal, April 1999

  • Marconi, Umberto Marini Bettolo; Tarazona, Pedro
  • The Journal of Chemical Physics, Vol. 110, Issue 16
  • DOI: 10.1063/1.478705

Improved Side Chain Dynamics in MARTINI Simulations of Protein–Lipid Interfaces
journal, April 2016

  • Herzog, Florian A.; Braun, Lukas; Schoen, Ingmar
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 5
  • DOI: 10.1021/acs.jctc.6b00122

Multiscale modeling of biomolecular systems: in serial and in parallel
journal, April 2007

  • Ayton, Gary S.; Noid, Will G.; Voth, Gregory A.
  • Current Opinion in Structural Biology, Vol. 17, Issue 2
  • DOI: 10.1016/j.sbi.2007.03.004

How Fast-Folding Proteins Fold
journal, October 2011

Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

Enantiomers of phospholipids and cholesterol: A key to decipher lipid‐lipid interplay in membrane
journal, December 2019

  • Hanashima, Shinya; Yano, Yo; Murata, Michio
  • Chirality, Vol. 32, Issue 3
  • DOI: 10.1002/chir.23171

The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

  • Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 5
  • DOI: 10.1021/ct700324x

A Leap-frog Algorithm for Stochastic Dynamics
journal, March 1988

A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts
journal, November 2005

  • Berjanskii, Mark V.; Wishart, David S.
  • Journal of the American Chemical Society, Vol. 127, Issue 43
  • DOI: 10.1021/ja054842f

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015

Computational reconstruction of atomistic protein structures from coarse-grained models
journal, January 2020

  • Badaczewska-Dawid, Aleksandra E.; Kolinski, Andrzej; Kmiecik, Sebastian
  • Computational and Structural Biotechnology Journal, Vol. 18
  • DOI: 10.1016/j.csbj.2019.12.007

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998

  • MacKerell, A. D.; Bashford, D.; Bellott, M.
  • The Journal of Physical Chemistry B, Vol. 102, Issue 18
  • DOI: 10.1021/jp973084f

GLIMPS: A Machine Learning Approach to Resolution Transformation for Multiscale Modeling
journal, December 2021

  • Louison, Keverne A.; Dryden, Ian L.; Laughton, Charles A.
  • Journal of Chemical Theory and Computation, Vol. 17, Issue 12
  • DOI: 10.1021/acs.jctc.1c00735

Unified Approach for Molecular Dynamics and Density-Functional Theory
journal, November 1985

The small GTPases K-Ras, N-Ras, and H-Ras have distinct biochemical properties determined by allosteric effects
journal, June 2017

  • Johnson, Christian W.; Reid, Derion; Parker, Jillian A.
  • Journal of Biological Chemistry, Vol. 292, Issue 31
  • DOI: 10.1074/jbc.M117.778886

CG2AT2: an Enhanced Fragment-Based Approach for Serial Multi-scale Molecular Dynamics Simulations
journal, September 2021

  • Vickery, Owen N.; Stansfeld, Phillip J.
  • Journal of Chemical Theory and Computation, Vol. 17, Issue 10
  • DOI: 10.1021/acs.jctc.1c00295

Dynamic properties of the Ras switch I region and its importance for binding to effectors
journal, April 2001

  • Spoerner, M.; Herrmann, C.; Vetter, I. R.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 9
  • DOI: 10.1073/pnas.081441398

RAS isoforms and mutations in cancer at a glance
journal, March 2016

  • Hobbs, G. Aaron; Der, Channing J.; Rossman, Kent L.
  • Journal of Cell Science, Vol. 129, Issue 7
  • DOI: 10.1242/jcs.182873

ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field
journal, July 2020

  • Zhang, Xiaohua; Sundram, Shiv; Oppelstrup, Tomas
  • The Journal of Chemical Physics, Vol. 153, Issue 4
  • DOI: 10.1063/5.0014500

Perspective on the Martini model
journal, January 2013

  • Marrink, Siewert J.; Tieleman, D. Peter
  • Chemical Society Reviews, Vol. 42, Issue 16
  • DOI: 10.1039/c3cs60093a

Coarse-grained simulations of proton-dependent conformational changes in lactose permease
journal, May 2016

  • Jewel, Yead; Dutta, Prashanta; Liu, Jin
  • Proteins: Structure, Function, and Bioinformatics, Vol. 84, Issue 8
  • DOI: 10.1002/prot.25053

Do all backbone polar groups in proteins form hydrogen bonds?
journal, July 2005

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks
journal, June 2013

Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity
journal, August 2020

  • Ingólfsson, Helgi I.; Bhatia, Harsh; Zeppelin, Talia
  • The Journal of Physical Chemistry B, Vol. 124, Issue 36
  • DOI: 10.1021/acs.jpcb.0c03368

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

Effects of Natural and Enantiomeric Cholesterol on the Thermotropic Phase Behavior and Structure of Egg Sphingomyelin Bilayer Membranes
journal, February 2003

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

  • Darden, Tom; York, Darrin; Pedersen, Lee
  • The Journal of Chemical Physics, Vol. 98, Issue 12
  • DOI: 10.1063/1.464397

From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
journal, May 2007

  • Heath, Allison P.; Kavraki, Lydia E.; Clementi, Cecilia
  • Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 3
  • DOI: 10.1002/prot.21371

Coarse-grained stochastic processes for microscopic lattice systems
journal, January 2003

  • Katsoulakis, M. A.; Majda, A. J.; Vlachos, D. G.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 3
  • DOI: 10.1073/pnas.242741499

Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins
journal, February 2017

  • Poma, Adolfo B.; Cieplak, Marek; Theodorakis, Panagiotis E.
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 3
  • DOI: 10.1021/acs.jctc.6b00986

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

Force field design for metalloproteins
journal, October 1991

  • Hoops, Stephen C.; Anderson, Kenneth W.; Merz, Kenneth M.
  • Journal of the American Chemical Society, Vol. 113, Issue 22
  • DOI: 10.1021/ja00022a010

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
journal, August 2012

  • Best, Robert B.; Zhu, Xiao; Shim, Jihyun
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300400x

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

  • Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
  • The Journal of Physical Chemistry B, Vol. 108, Issue 2
  • DOI: 10.1021/jp036508g

Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations
journal, March 2013

  • Wassenaar, Tsjerk A.; Ingólfsson, Helgi I.; Prieß, Marten
  • The Journal of Physical Chemistry B, Vol. 117, Issue 13
  • DOI: 10.1021/jp311533p

The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations
journal, August 2013

  • Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
  • DOI: 10.1002/wcms.1169

Multiscale simulation approaches to modeling drug–protein binding
journal, April 2020

  • Jagger, Benjamin R.; Kochanek, Sarah E.; Haldar, Susanta
  • Current Opinion in Structural Biology, Vol. 61
  • DOI: 10.1016/j.sbi.2020.01.014

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition
journal, August 2009

  • Periole, Xavier; Cavalli, Marco; Marrink, Siewert-Jan
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct9002114

Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction
journal, March 2021

A series of PDB-related databanks for everyday needs
journal, October 2014

  • Touw, Wouter G.; Baakman, Coos; Black, Jon
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1028

Entropic forces drive clustering and spatial localization of influenza A M2 during viral budding
journal, August 2018

  • Madsen, Jesper J.; Grime, John M. A.; Rossman, Jeremy S.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 37
  • DOI: 10.1073/pnas.1805443115

Stereospecific requirement of cholesterol in the function of the serotonin1A receptor
journal, January 2014

  • Jafurulla, Md.; Rao, Bhagyashree D.; Sreedevi, Sugunan
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1838, Issue 1
  • DOI: 10.1016/j.bbamem.2013.08.015

Enantiospecific Interactions between Cholesterol and Phospholipids
journal, January 2008

  • Alakoskela, Juha-Matti; Sabatini, Karen; Jiang, Xin
  • Langmuir, Vol. 24, Issue 3
  • DOI: 10.1021/la702909q

Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane
journal, September 2020

  • Van, Que N.; López, Cesar A.; Tonelli, Marco
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 39
  • DOI: 10.1073/pnas.2006504117

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations
journal, May 2019

  • Alfonso-Prieto, Mercedes; Navarini, Luciano; Carloni, Paolo
  • Frontiers in Molecular Biosciences, Vol. 6
  • DOI: 10.3389/fmolb.2019.00029

Chiral Recognition of Lipid Bilayer Membranes by Supramolecular Assemblies of Peptide Amphiphiles
journal, May 2019

Hybrid Atomistic and Coarse-Grained Model for Surfactants in Apolar Solvents
journal, September 2019

Adaptive Resolution Simulation of MARTINI Solvents
journal, May 2014

  • Zavadlav, Julija; Melo, Manuel N.; Cunha, Ana V.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 6
  • DOI: 10.1021/ct5001523

Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
journal, November 2005

VMD: Visual molecular dynamics
journal, February 1996

PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification
journal, October 2010

  • Han, Wei; Wan, Cheuk-Kin; Jiang, Fan
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 11
  • DOI: 10.1021/ct1003127

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
journal, April 2011

  • Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart
  • Journal of Computational Chemistry, Vol. 32, Issue 9
  • DOI: 10.1002/jcc.21777

Reconstruction of atomistic details from coarse-grained structures
journal, January 2010

  • Rzepiela, Andrzej J.; Schäfer, Lars V.; Goga, Nicolae
  • Journal of Computational Chemistry
  • DOI: 10.1002/jcc.21415

Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations
journal, April 2012

  • Predeus, Alexander V.; Gul, Seref; Gopal, Srinivasa M.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 29
  • DOI: 10.1021/jp300129u

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
journal, May 2013

  • Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik
  • International Journal of Molecular Sciences, Vol. 14, Issue 5
  • DOI: 10.3390/ijms14059893

Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins
journal, January 2022

  • Ingólfsson, Helgi I.; Neale, Chris; Carpenter, Timothy S.
  • Proceedings of the National Academy of Sciences, Vol. 119, Issue 1
  • DOI: 10.1073/pnas.2113297119

Quasicontinuum analysis of defects in solids
journal, June 1996

Ras and the Plasma Membrane: A Complicated Relationship
journal, December 2017

  • Zhou, Yong; Prakash, Priyanka; Gorfe, Alemayehu A.
  • Cold Spring Harbor Perspectives in Medicine, Vol. 8, Issue 10
  • DOI: 10.1101/cshperspect.a031831

Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions
journal, July 2016

  • Kreis, Karsten; Potestio, Raffaello; Kremer, Kurt
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 8
  • DOI: 10.1021/acs.jctc.6b00440

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977

  • Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
  • Journal of Computational Physics, Vol. 23, Issue 3
  • DOI: 10.1016/0021-9991(77)90098-5

Methionine 170 is an Environmentally Sensitive Membrane Anchor in the Disordered HVR of K-Ras4B
journal, October 2018

A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
journal, January 1982

  • Swope, William C.; Andersen, Hans C.; Berens, Peter H.
  • The Journal of Chemical Physics, Vol. 76, Issue 1
  • DOI: 10.1063/1.442716

Generalizable coordination of large multiscale workflows: challenges and learnings at scale
conference, November 2021

  • Bhatia, Harsh; Di Natale, Francesco; Moon, Joseph Y.
  • SC '21: The International Conference for High Performance Computing, Networking, Storage and Analysis, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
  • DOI: 10.1145/3458817.3476210

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly
journal, December 2005

  • Praprotnik, Matej; Delle Site, Luigi; Kremer, Kurt
  • The Journal of Chemical Physics, Vol. 123, Issue 22
  • DOI: 10.1063/1.2132286

Metal Ion Modeling Using Classical Mechanics
journal, January 2017

Improved Modeling of Halogenated Ligand–Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields
journal, November 2018

  • Lin, Fang-Yu; MacKerell, Alexander D.
  • Journal of Chemical Information and Modeling, Vol. 59, Issue 1
  • DOI: 10.1021/acs.jcim.8b00616

Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy
journal, December 2012

Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics
journal, December 2005

Mixed Atomistic and Coarse-Grained Molecular Dynamics:  Simulation of a Membrane-Bound Ion Channel
journal, July 2006

  • Shi, Qiang; Izvekov, Sergei; Voth, Gregory A.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 31
  • DOI: 10.1021/jp062700h

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding
journal, February 2008

Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors
journal, January 2022

  • Reisjalali, Maryam; Manurung, Rex; Carbone, Paola
  • Molecular Systems Design & Engineering, Vol. 7, Issue 3
  • DOI: 10.1039/D1ME00165E

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

  • Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
  • The Journal of Physical Chemistry B, Vol. 114, Issue 23
  • DOI: 10.1021/jp101759q

Multi-level adaptive solutions to boundary-value problems
journal, May 1977

Structures of N-terminally processed KRAS provide insight into the role of N-acetylation
journal, July 2019

  • Dharmaiah, Srisathiyanarayanan; Tran, Timothy H.; Messing, Simon
  • Scientific Reports, Vol. 9, Issue 1
  • DOI: 10.1038/s41598-019-46846-w

Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?
journal, January 2021

  • Cui, Qiang; Pal, Tanmoy; Xie, Luke
  • The Journal of Physical Chemistry B, Vol. 125, Issue 3
  • DOI: 10.1021/acs.jpcb.0c09898

Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations
journal, April 2021

  • Bhatia, Harsh; Carpenter, Timothy S.; Ingólfsson, Helgi I.
  • Nature Machine Intelligence, Vol. 3, Issue 5
  • DOI: 10.1038/s42256-021-00327-w

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
journal, July 2009

Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21N-ras and the Resulting GTP Electronic Density
journal, April 2019

  • Tichauer, Ruth H.; Favre, Gilles; Cabantous, Stéphanie
  • The Journal of Physical Chemistry B, Vol. 123, Issue 18
  • DOI: 10.1021/acs.jpcb.9b02660

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
journal, March 2015

  • Hopkins, Chad W.; Le Grand, Scott; Walker, Ross C.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 4
  • DOI: 10.1021/ct5010406

The protonation states of GTP and GppNHp in Ras proteins
journal, March 2018

  • Mann, Daniel; Güldenhaupt, Jörn; Schartner, Jonas
  • Journal of Biological Chemistry, Vol. 293, Issue 11
  • DOI: 10.1074/jbc.RA117.001110

A novel multiscale scheme to accelerate atomistic simulations of bio-macromolecules by adaptively driving coarse-grained coordinates
journal, March 2020

  • Wu, Kai; Xu, Shun; Wan, Biao
  • The Journal of Chemical Physics, Vol. 152, Issue 11
  • DOI: 10.1063/1.5135309

Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover
journal, January 2021

  • Jarin, Zack; Newhouse, James; Voth, Gregory A.
  • Journal of Chemical Theory and Computation, Vol. 17, Issue 2
  • DOI: 10.1021/acs.jctc.0c00638

Water's Hydrogen Bonds in the Hydrophobic Effect:  A Simple Model
journal, December 2005

  • Xu, Huafeng; Dill, Ken A.
  • The Journal of Physical Chemistry B, Vol. 109, Issue 49
  • DOI: 10.1021/jp0526750

Improved Parameters for the Martini Coarse-Grained Protein Force Field
journal, November 2012

  • de Jong, Djurre H.; Singh, Gurpreet; Bennett, W. F. Drew
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300646g

Comparison of Phosphatidylcholine Vesicle Properties Related to Geometrical Isomerism†
journal, January 2006

  • Ferreri, Carla; Pierotti, Silvia; Barbieri, Andrea
  • Photochemistry and Photobiology, Vol. 82, Issue 1
  • DOI: 10.1562/2005-06-01-RA-559

Multivalent assembly of KRAS with the RAS-binding and cysteine-rich domains of CRAF on the membrane
journal, May 2020

  • Fang, Zhenhao; Lee, Ki-Young; Huo, Ku-Geng
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 22
  • DOI: 10.1073/pnas.1914076117

Molecular Dynamics Simulation for All
journal, September 2018

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer
conference, November 2019

  • Di Natale, Francesco; Bhatia, Harsh; Carpenter, Timothy S.
  • SC '19: The International Conference for High Performance Computing, Networking, Storage, and Analysis, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
  • DOI: 10.1145/3295500.3356197

Adaptive resolution simulation of an atomistic protein in MARTINI water
journal, February 2014

  • Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.
  • The Journal of Chemical Physics, Vol. 140, Issue 5
  • DOI: 10.1063/1.4863329

All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
journal, January 2000

Machine learning approach for accurate backmapping of coarse-grained models to all-atom models
journal, January 2020

  • An, Yaxin; Deshmukh, Sanket A.
  • Chemical Communications, Vol. 56, Issue 65
  • DOI: 10.1039/D0CC02651D

Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations
journal, December 2007

  • Michel, Julien; Orsi, Mario; Essex, Jonathan W.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 3
  • DOI: 10.1021/jp076142y

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm
journal, February 2018

  • Zavadlav, Julija; Marrink, Siewert J.; Praprotnik, Matej
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 3
  • DOI: 10.1021/acs.jctc.7b01129

Monte Carlo studies of the dielectric properties of water-like models
journal, September 1973

How stereochemistry of lipid components can affect lipid organization and the route of liposome internalization into cells
journal, January 2021

  • Borocci, Stefano; Bozzuto, Giuseppina; Bombelli, Cecilia
  • Nanoscale, Vol. 13, Issue 27
  • DOI: 10.1039/D1NR02175C

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes
journal, July 2008

  • Mukherjee, Arnab; Lavery, Richard; Bagchi, Biman
  • Journal of the American Chemical Society, Vol. 130, Issue 30
  • DOI: 10.1021/ja8001666

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field
journal, September 2018

  • Carpenter, Timothy S.; López, Cesar A.; Neale, Chris
  • Journal of Chemical Theory and Computation, Vol. 14, Issue 11
  • DOI: 10.1021/acs.jctc.8b00496

The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes
journal, May 2020

  • Ngo, Van A.; Sarkar, Sumantra; Neale, Chris
  • The Journal of Physical Chemistry B, Vol. 124, Issue 26
  • DOI: 10.1021/acs.jpcb.0c02642

Helix formation and stability in membranes
journal, October 2018

  • McKay, Matthew J.; Afrose, Fahmida; Koeppe, Roger E.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1860, Issue 10
  • DOI: 10.1016/j.bbamem.2018.02.010

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
journal, November 2013

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992

  • Miyamoto, Shuichi; Kollman, Peter A.
  • Journal of Computational Chemistry, Vol. 13, Issue 8
  • DOI: 10.1002/jcc.540130805

Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs
journal, January 2019

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
journal, April 2011

  • Michaud-Agrawal, Naveen; Denning, Elizabeth J.; Woolf, Thomas B.
  • Journal of Computational Chemistry, Vol. 32, Issue 10
  • DOI: 10.1002/jcc.21787

Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies
journal, January 2020

  • Sarkar, Sunipa; Rajdev, Priya; Singh, Prashant Chandra
  • Physical Chemistry Chemical Physics, Vol. 22, Issue 27
  • DOI: 10.1039/D0CP01548B

Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations 1 1Edited by J. M. Thornton
journal, November 1999

  • Pal, Debnath; Chakrabarti, Pinak
  • Journal of Molecular Biology, Vol. 294, Issue 1
  • DOI: 10.1006/jmbi.1999.3217

Martini Coarse-Grained Force Field: Extension to DNA
journal, July 2015

  • Uusitalo, Jaakko J.; Ingólfsson, Helgi I.; Akhshi, Parisa
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 8
  • DOI: 10.1021/acs.jctc.5b00286

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation
journal, February 2021

The solution structure of the Raf-1 cysteine-rich domain: a novel ras and phospholipid binding site.
journal, August 1996

  • Mott, H. R.; Carpenter, J. W.; Zhong, S.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 16
  • DOI: 10.1073/pnas.93.16.8312

A smooth particle mesh Ewald method
journal, November 1995

  • Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
  • The Journal of Chemical Physics, Vol. 103, Issue 19
  • DOI: 10.1063/1.470117

Accurate simulation of protein dynamics in solution.
journal, October 1988

  • Levitt, M.; Sharon, R.
  • Proceedings of the National Academy of Sciences, Vol. 85, Issue 20
  • DOI: 10.1073/pnas.85.20.7557

Backmapping triangulated surfaces to coarse-grained membrane models
journal, May 2020

  • Pezeshkian, Weria; König, Melanie; Wassenaar, Tsjerk A.
  • Nature Communications, Vol. 11, Issue 1
  • DOI: 10.1038/s41467-020-16094-y

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
journal, January 2014

  • Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 2
  • DOI: 10.1021/ct400617g

The Martini Model in Materials Science
journal, May 2021

  • Alessandri, Riccardo; Grünewald, Fabian; Marrink, Siewert J.
  • Advanced Materials, Vol. 33, Issue 24
  • DOI: 10.1002/adma.202008635

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
journal, October 2016

  • Shirts, Michael R.; Klein, Christoph; Swails, Jason M.
  • Journal of Computer-Aided Molecular Design, Vol. 31, Issue 1
  • DOI: 10.1007/s10822-016-9977-1

Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations
journal, April 2015

  • Wassenaar, Tsjerk A.; Ingólfsson, Helgi I.; Böckmann, Rainer A.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 5
  • DOI: 10.1021/acs.jctc.5b00209

The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling
journal, March 2020

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
journal, January 2011

  • Rzepiela, Andrzej J.; Louhivuori, Martti; Peter, Christine
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 22
  • DOI: 10.1039/c0cp02981e

Adaptive resolution simulations of biomolecular systems
journal, September 2017

  • Zavadlav, Julija; Bevc, Staš; Praprotnik, Matej
  • European Biophysics Journal, Vol. 46, Issue 8
  • DOI: 10.1007/s00249-017-1248-0

Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain
journal, May 2018

The α-helix folds on the millisecond time scale
journal, June 1999

  • Clarke, David T.; Doig, Andrew J.; Stapley, Benjamin J.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 13
  • DOI: 10.1073/pnas.96.13.7232
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