Building complex membranes with Martini 3
Tugba Nur Ozturk, Melanie König, Timothy S. Carpenter, Kasper B. Pedersen, Tsjerk A. Wassenaar, Helgi I. Ingólfsson, Siewert J. Marrink 
Methods in Enzymology (2024)

Tutorial data

Multiscale simulations reveal TDP-43 molecular level interactions driving condensation 
Helgi I. Ingólfsson, Azamat Rizuan, Xikun Liu, Priyesh Mohanty, Paulo C.T. Souza, Siewert J. Marrink, Michael T. Bowers, Jeetain Mittal, Joel Berry
Biophysical Journal (2023).

Data

Machine Learning-driven Multiscale Modeling: Bridging the Scales With a Next Generation Simulation Infrastructure
Helgi I. Ingólfsson, Harsh Bhatia, Fikret Aydin, Tomas Oppelstrup, Cesar A López, Liam G. Stanton, Timothy S. Carpenter, Sergio Wong, Francesco Di Natale, Xiaohua Zhang, Joseph Y. Moon, Christopher B. Stanley, Joseph R. Chavez, Kien Nguyen, Gautham Dharuman, Violetta Burns, Rebika Shrestha, Debanjan Goswami, Gulcin Gulten, Que N. Van, Arvind Ramanathan, Brian Van Essen, Nicolas W. Hengartner, Andrew G. Stephen, Thomas Turbyville, Peer-Timo Bremer, S. Gnanakaran, James N. Glosli, Felice C. Lightstone, Dwight V. Nissley, Frederick H. Streitz
J. Chem. Theory Comput. (2023) Accepted.

Data

Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Proteins

Helgi I. Inglfsson, Chris Neale, Timothy S. Carpenter, Rebika Shrestha, Cesar A Lopez, Timothy H. Tran, Tomas Oppelstrup, Harsh Bhatia, Liam G. Stanton, Xiaohua Zhang, Shiv Sundram, Francesco Di Natale, Animesh Agarwal, Gautham Dharuman, Sara I. L. Kokkila Schumacher, Thomas Turbyville, Gulcin Gulten, Que N. Van, Debanjan Goswami, Frantz Jean Francios, Constance Agamasu, De Chen, Jeevapani J. Hettige, Timothy Travers, Sumantra Sarkar, Michael P. Surh, Yue Yang, Adam Moody, Shusen Liu, Brian C. Van Essen, Arthur F. Voter, Arvind Ramanathan, Nicolas W. Hengartner,  Dhirendra K. Simanshu, Andrew G. Stephen, Peer-Timo Bremer, S. Gnanakaran, James N. Glosli, Felice C. Lightstone, Frank McCormick, Dwight V. Nissley, Frederick H. Streitz. 
Proceedings of the National Academy of Sciences (2022) 119 (1) e2113297119.

Data

Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity
H. I. Ingólfsson, H. Bhatia, T. Zeppelin, W. F. D. Bennett, K. A. Carpenter, P.-C. Hsu, G. Dharuman, P.-T. Bremer, B. Schiøtt, F. C. Lightstone, and T. S. Carpenter
J. Phys. Chem. B (2020), 124, 36, 7819–7829.

Data

Membrane interactions of the globular domain and the hypervariable region of KRAS4b define its unique diffusion behavior

Debanjan Goswami, De Chen, Yue Yang, Prabhakar R. Gudla, John Columbus, Karen Worthy, Megan Rigby, Madeline Wheeler, Suman Mukhopadhyay, Katie Powell, William Burgan, Vanessa Wall, Dominic Esposito, Dhirendra Simanshu, Felice C. Lightstone, Dwight V. Nissley, Frank McCormick, Thomas Turbyville
eLife (2020), 9: e47654.

Data  LLNL-MI-793014

MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes
Harsh Bhatia, Helgi I. Ingólfsson, Timothy S. Carpenter, Felice C. Lightstone, Peer-Timo Bremer
Journal of Chemical Theory and Computation (2019) 15, 11, 6411-6421.

Data

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field
T. S. Carpenter, C. A. López, C. Neale, C. Montour, H. I. Ingólfsson, F. Di Natale, F. C. Lightstone, and S. Gnanakaran
Journal of Chemical Theory and Computation (2018) 14, 6050-6062.

Data

Computational Lipidomics of the Neuronal Plasma Membrane
Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J. Marrink, Felice C. Lightstone
Biophysical Journal (2017) 113(10).

Data

A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
Brian J. Bennion, Sebnem G. Essiz, Edmond Y. Lau, Jean-Luc Fattebert, Aiyana Emigh, Felice C. Lightstone
PLoS ONE  (2014) 10(4): e0121092.

Data - soman phosphonylation of human AChE, apo and soman-adducted NAMD topology files, PDB structure files, Figures 5 and 6 source data.  LLNL-WEB-667081

 

Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines
Montiago X. LaBute, Xiaohua Zhang, Jason Lenderman, Brian J. Bennion, Sergio E. Wong, Felice C. Lightstone
PLoS ONE (2014) 9(9): e106298.

Data - drug-target protein docking scores, top-ranked drug docking poses.  LLNL-WEB-655656