Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations

por Spiriti, Justin, Zuckerman, Daniel M.
Publicado 2014

Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratio

por Anandakrishnan, Ramu, Zuckerman, Daniel M.
Publicado 2017

Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models

por Suárez, Ernesto, Adelman, Joshua L., Zuckerman, Daniel M.
Publicado 2016

EmrE reminds us to expect the unexpected in membrane transport

por Grabe, Michael, Zuckerman, Daniel M., Rosenberg, John M.
Publicado 2019

Quantifying cooperative multisite binding in the hub protein LC8 through Bayesian inference

por Estelle, Aidan B., George, August, Barbar, Elisar J., Zuckerman, Daniel M.
Publicado 2023

Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

por Spiriti, Justin, Subramanian, Sundar Raman, Palli, Rohith, Wu, Maria, Zuckerman, Daniel M.
Publicado 2019

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

por George, August, Bisignano, Paola, Rosenberg, John M., Grabe, Michael, Zuckerman, Daniel M.
Publicado 2020

Morphodynamical cell state description via live-cell imaging trajectory embedding

por Copperman, Jeremy, Gross, Sean M., Chang, Young Hwan, Heiser, Laura M., Zuckerman, Daniel M.
Publicado 2023

A kinetic mechanism for enhanced selectivity of membrane transport

por Bisignano, Paola, Lee, Michael A., George, August, Zuckerman, Daniel M., Grabe, Michael, Rosenberg, John M.
Publicado 2020

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories

por Suárez, Ernesto, Lettieri, Steven, Zwier, Matthew C., Stringer, Carsen A., Subramanian, Sundar Raman, Chong, Lillian T., Zuckerman, Daniel M.
Publicado 2014

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

por Donovan, Rory M., Tapia, Jose-Juan, Sullivan, Devin P., Faeder, James R., Murphy, Robert F., Dittrich, Markus, Zuckerman, Daniel M.
Publicado 2016

Vascular K(ATP) channel structural dynamics reveal regulatory mechanism by Mg-nucleotides

por Sung, Min Woo, Yang, Zhongying, Driggers, Camden M., Patton, Bruce L., Mostofian, Barmak, Russo, John D., Zuckerman, Daniel M., Shyng, Show-Ling
Publicado 2021

Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

por Flores, Jonathan A., Haddad, Bassam G., Dolan, Kimberly A., Myers, Janette B., Yoshioka, Craig C., Copperman, Jeremy, Zuckerman, Daniel M., Reichow, Steve L.
Publicado 2020

Structure of native lens connexin-46/50 intercellular channels by CryoEM

por Myers, Janette B., Haddad, Bassam G., O’Neill, Susan E., Chorev, Dror S., Yoshioka, Craig C., Robinson, Carol V., Zuckerman, Daniel M., Reichow, Steve L.
Publicado 2018

High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas(G12D) diffusion and trafficking

por Lee, Yerim, Phelps, Carey, Huang, Tao, Mostofian, Barmak, Wu, Lei, Zhang, Ying, Tao, Kai, Chang, Young Hwan, Stork, Philip JS, Gray, Joe W, Zuckerman, Daniel M, Nan, Xiaolin
Publicado 2019

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

por Dommer, Abigail, Casalino, Lorenzo, Kearns, Fiona, Rosenfeld, Mia, Wauer, Nicholas, Ahn, Surl-Hee, Russo, John, Oliveira, Sofia, Morris, Clare, Bogetti, Anthony, Trifan, Anda, Brace, Alexander, Sztain, Terra, Clyde, Austin, Ma, Heng, Chennubhotla, Chakra, Lee, Hyungro, Turilli, Matteo, Khalid, Syma, Tamayo-Mendoza, Teresa, Welborn, Matthew, Christensen, Anders, Smith, Daniel G. A., Qiao, Zhuoran, Sirumalla, Sai Krishna, O’Connor, Michael, Manby, Frederick, Anandkumar, Anima, Hardy, David, Phillips, James, Stern, Abraham, Romero, Josh, Clark, David, Dorrell, Mitchell, Maiden, Tom, Huang, Lei, McCalpin, John, Woods, Christopher, Gray, Alan, Williams, Matt, Barker, Bryan, Rajapaksha, Harinda, Pitts, Richard, Gibbs, Tom, Stone, John, Zuckerman, Daniel, Mulholland, Adrian, Miller, Thomas, Jha, Shantenu, Ramanathan, Arvind, Chong, Lillian, Amaro, Rommie
Publicado 2021

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

por Dommer, Abigail, Casalino, Lorenzo, Kearns, Fiona, Rosenfeld, Mia, Wauer, Nicholas, Ahn, Surl-Hee, Russo, John, Oliveira, Sofia, Morris, Clare, Bogetti, Anthony, Trifan, Anda, Brace, Alexander, Sztain, Terra, Clyde, Austin, Ma, Heng, Chennubhotla, Chakra, Lee, Hyungro, Turilli, Matteo, Khalid, Syma, Tamayo-Mendoza, Teresa, Welborn, Matthew, Christensen, Anders, Smith, Daniel GA, Qiao, Zhuoran, Sirumalla, Sai K, O’Connor, Michael, Manby, Frederick, Anandkumar, Anima, Hardy, David, Phillips, James, Stern, Abraham, Romero, Josh, Clark, David, Dorrell, Mitchell, Maiden, Tom, Huang, Lei, McCalpin, John, Woods, Christopher, Gray, Alan, Williams, Matt, Barker, Bryan, Rajapaksha, Harinda, Pitts, Richard, Gibbs, Tom, Stone, John, Zuckerman, Daniel M., Mulholland, Adrian J., Miller, Thomas, Jha, Shantenu, Ramanathan, Arvind, Chong, Lillian, Amaro, Rommie E
Publicado 2022