Search Results - "Sultan, Mohammad M"

tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables by M. Sultan, Mohammad, Pande, Vijay S

“…Metadynamics is a powerful enhanced molecular dynamics sampling method that accelerates simulations by adding history-dependent multidimensional Gaussians…”
Get full text

MSMBuilder: Statistical Models for Biomolecular Dynamics by Harrigan, Matthew P., Sultan, Mohammad M., Hernández, Carlos X., Husic, Brooke E., Eastman, Peter, Schwantes, Christian R., Beauchamp, Kyle A., McGibbon, Robert T., Pande, Vijay S.

“…MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis…”
Get full text

Towards simple kinetic models of functional dynamics for a kinase subfamily by Sultan, Mohammad M., Kiss, Gert, Pande, Vijay S.

“…Kinases are ubiquitous enzymes involved in the regulation of critical cellular pathways. However, in silico modelling of the conformational ensembles of these…”
Get full text

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics by Sultan, Mohammad M, Wayment-Steele, Hannah K, Pande, Vijay S

“…Variational autoencoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single nonlinear embedding. In…”
Get full text

Optimized parameter selection reveals trends in Markov state models for protein folding by Husic, Brooke E, McGibbon, Robert T, Sultan, Mohammad M, Pande, Vijay S

“…As molecular dynamics simulations access increasingly longer time scales, complementary advances in the analysis of biomolecular time-series data are…”
Get more information

Allosteric pathways in imidazole glycerol phosphate synthase by Rivalta, Ivan, Sultan, Mohammad M, Lee, Ning-Shiuan, Manley, Gregory A, Loria, J. Patrick, Batista, Victor S

“…Protein allosteric pathways are investigated in the imidazole glycerol phosphate synthase heterodimer in an effort to elucidate how the effector (PRFAR,…”
Get full text

Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain by Sultan, Mohammad M., Denny, Rajiah Aldrin, Unwalla, Ray, Lovering, Frank, Pande, Vijay S.

“…Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK…”
Get full text

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations by Sultan, Mohammad M, Kiss, Gert, Shukla, Diwakar, Pande, Vijay S

“…Given the large number of crystal structures and NMR ensembles that have been solved to date, classical molecular dynamics (MD) simulations have become…”
Get full text

Electrostatic Effects on Proton Coupled Electron Transfer in Oxomanganese Complexes Inspired by the Oxygen-Evolving Complex of Photosystem II by Amin, Muhamed, Vogt, Leslie, Vassiliev, Serguei, Rivalta, Ivan, Sultan, Mohammad M, Bruce, Doug, Brudvig, Gary W, Batista, Victor S, Gunner, M. R

“…The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the…”
Get full text

Compositional Deep Probabilistic Models of DNA-Encoded Libraries by Chen, Benson, Sultan, Mohammad M., Karaletsos, Theofanis

“…DNA-encoded library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly efficient screening…”
Get full text

DEL-Dock: Molecular Docking-Enabled Modeling of DNA-Encoded Libraries by Shmilovich, Kirill, Chen, Benson, Karaletsos, Theofanis, Sultan, Mohammad M.

“…DNA-encoded library (DEL) technology has enabled significant advances in hit identification by enabling efficient testing of combinatorially generated…”
Get full text

Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems by Sultan, Mohammad M, Pande, Vijay S

“…We recently showed that the time-structure-based independent component analysis method from Markov state model literature provided a set of variationally…”
Get full text

A Minimum Variance Clustering Approach Produces Robust and Interpretable Coarse-Grained Models by Husic, Brooke E, McKiernan, Keri A, Wayment-Steele, Hannah K, Sultan, Mohammad M, Pande, Vijay S

“…Markov state models (MSMs) are a powerful framework for the analysis of molecular dynamics data sets, such as protein folding simulations, because of their…”
Get full text

MSMExplorer: Data Visualizations for Biomolecular Dynamics by X. Hernández, Carlos, P. Harrigan, Matthew, M. Sultan, Mohammad, S. Pande, Vijay

Get full text

Lessons from 8 Milliseconds of Aggregated Kinase Molecular Dynamics Simulations by Sultan, Mohammad M., Pande, Vijay

Get full text

Computational Evaluation of Mutational Effects on Kinase Dynamics by Sultan, Mohammad M., Pande, Vijay

Get full text

Supervised Learning on Markov States as a Method for Gaining Insight into Protein Allostery by Sultan, Mohammad M.

Get full text

Prevalence of High-Grade Dysplasia in Diminutive Colon Polyps at a Community-Based Endoscopy Center: A Retrospective Analysis and Literature Review: 275 by Guharoy, Victor, Evans, Robert J, Lamoureux, Mary, Mohammad, Sultan M.

Get full text

Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles by Piwonski, Hubert M, Goomanovsky, Mila, Bensimon, David, Horovitz, Amnon, Haran, Gilad

“…Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule…”
Get full text

Optimize an MRI Gauss Gun by Sultan, Mohammad M

“…MRI-based navigation and propulsion of millirobots is a new and promising approach for minimally invasive therapies. The strong constant magnetic field inside…”
Get full text