Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Privacy-aware community infrastructureResearch graph
References from cryoWEight : Conformational ensembles from cryo-EM particle images with weighted ensemble simulations. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1016/j.tibs.2014.10.005
10.1016/j.tibs.2014.10.005 · External reference
10.1038/s41586-020-2829-0
10.1038/s41586-020-2829-0 · External reference
Editorial overview: Cryo-electron microscopy
10.1016/j.sbi.2024.102937 · 2024 · External reference
10.1016/j.bpj.2016.02.001
10.1016/j.bpj.2016.02.001 · External reference
10.1126/science.1251652
10.1126/science.1251652 · External reference
10.7554/elife.03678
10.7554/elife.03678 · External reference
10.1146/annurev-biochem-032620-110705
10.1146/annurev-biochem-032620-110705 · External reference
10.1016/j.jsb.2012.09.006
10.1016/j.jsb.2012.09.006 · External reference
cryosparc: algorithms for rapid unsupervised cryo-em structure determination
10.1038/nmeth.4169 · 2017 · External reference
10.1016/j.cell.2022.02.016
10.1016/j.cell.2022.02.016 · External reference
10.1016/j.drudis.2019.12.006
10.1016/j.drudis.2019.12.006 · External reference
10.1038/nrd.2018.77
10.1038/nrd.2018.77 · External reference
10.1038/nature09206
10.1038/nature09206 · External reference
Structural dynamics: review of time-resolved cryo-em
2022 · External reference
10.1016/j.sbi.2023.102626
10.1016/j.sbi.2023.102626 · External reference
Single-particle cryo-em and molecular dynamics simulations: A perfect match
10.1016/j.sbi.2024.102825 · 2024 · External reference
Molecular dynamics to predict cryoem: Capturing transitions and short-lived conformational states of biomolecules
10.3389/fmolb.2021.641208 · 2021 · External reference
Integrating cryo-electron microscopy and molecular dynamics simulations to investigate membrane binding of influenza virus fusion peptides
10.1021/jacs.4c18441 · 2025 · External reference
10.1016/j.neuron.2018.08.011
10.1016/j.neuron.2018.08.011 · External reference
10.1016/j.coph.2010.09.008
10.1016/j.coph.2010.09.008 · External reference
10.1126/science.1187409
10.1126/science.1187409 · External reference
10.1146/annurev-physchem-083122-125941
10.1146/annurev-physchem-083122-125941 · External reference
En-hanced sampling methods for molecular dynamics simulations
2022 · External reference
What makes a kinase promiscuous for inhibitors?
10.1016/j.chembiol.2018.11.005 · 2019 · External reference
Activation pathway of src kinase reveals intermediate states as targets for drug design
10.1038/ncomms4397 · 2014 · External reference
10.1016/j.sbi.2012.11.002
10.1016/j.sbi.2012.11.002 · External reference
10.1126/science.1208351
10.1126/science.1208351 · External reference
10.1021/ja202726y
10.1021/ja202726y · External reference
10.1073/pnas.1103547108
10.1073/pnas.1103547108 · External reference
Prediction of threonine-tyrosine kinase receptor–ligand unbinding kinetics with multi-scale milestoning and metadynamics
10.1021/acs.jpclett.4c02332 · 2024 · External reference
10.1016/j.sbi.2016.11.019
10.1016/j.sbi.2016.11.019 · External reference
Directionally negative friction: A method for enhanced sampling of rare event kinetics
10.1063/1.2841102 · 2008 · External reference
10.1529/biophysj.107.111658
10.1529/biophysj.107.111658 · External reference
Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM)
2018 · External reference
10.1016/s0006-3495(96)79552-8
10.1016/s0006-3495(96)79552-8 · External reference
10.1146/annurev-biophys-070816-033834
10.1146/annurev-biophys-070816-033834 · External reference
10.1063/1.3306345
10.1063/1.3306345 · External reference
Unsupervised learning of progress coordinates during weighted ensemble simulations: Application to ntl9 protein folding
10.1021/acs.jctc.4c01136 · 2025 · External reference
Deepwest: Deep learning of kinetic models with the weighted ensemble simulation toolkit for enhanced sampling
10.1021/acs.jctc.2c00282 · 2023 · External reference
Discriminant analysis optimizes progress coordinate in weighted ensemble simulations of rare event kinetics
10.1063/5.0276623 · 2025 · External reference
10.1021/jacs.8b10735
10.1021/jacs.8b10735 · External reference
Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations
10.1039/c8sc04811h · 2019 · External reference
10.1021/acs.jcim.1c01540
10.1021/acs.jcim.1c01540 · External reference
Translocation of a single arg 9 peptide across a dopc/dopg (4: 1) model membrane using the weighted ensemble method
10.1038/s41598-023-28493-4 · 2023 · External reference
Molecular mechanism of ligand binding to he minor groove of dna
10.1021/acs.jpclett.3c00635 · 2023 · External reference
10.1021/acs.jcim.4c01435
10.1021/acs.jcim.4c01435 · External reference
A glycan gate controls opening of the sars-cov-2 spike protein
10.1038/s41557-021-00758-3 · 2021 · External reference
10.1101/2025.04.23.650329
10.1101/2025.04.23.650329 · External reference
Weighted ensemble simulation: Advances in methods, software, and applications
2025 · External reference
10.1063/1.5100521
10.1063/1.5100521 · External reference
10.1063/1.3456985
10.1063/1.3456985 · External reference
Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories
10.1016/j.bpj.2013.11.2285 · 2014 · External reference
Accelerated estimation of long-timescale kinetics by combining weighted ensemble simulation with markov model “microstates” using non-markovian theory
10.1016/j.bpj.2019.11.1099 · 2020 · External reference
Accurate estimation of protein folding and unfolding times: beyond markov state models
10.1021/acs.jctc.6b00339 · 2016 · External reference
10.1063/5.0215975
10.1063/5.0215975 · External reference
10.1063/1.4902240
10.1063/1.4902240 · External reference
10.1073/pnas.1525092113
10.1073/pnas.1525092113 · External reference
10.1016/j.jmb.2023.168020
10.1016/j.jmb.2023.168020 · External reference
Disentangling conformational states of macromolecules in 3d-em through likelihood optimization
10.1038/nmeth992 · 2007 · External reference
Unresolved reference
2010 · External reference
Cryodrgn: reconstruction of heterogeneous cryo-em structures using neural networks
10.1038/s41592-020-01049-4 · 2021 · External reference
10.1016/j.ymeth.2016.02.007
10.1016/j.ymeth.2016.02.007 · External reference
10.1073/pnas.1419276111
10.1073/pnas.1419276111 · External reference
10.1021/acs.jcim.9b01115
10.1021/acs.jcim.9b01115 · External reference
Recovery of conformational continuum from single-particle cryo-em images: Optimization of manifoldem informed by ground truth
10.1109/tci.2022.3174801 · 2022 · External reference
10.1107/s2059798325001469
10.1107/s2059798325001469 · External reference
10.1016/j.str.2011.10.003
10.1016/j.str.2011.10.003 · External reference
10.1016/j.jsb.2015.05.007
10.1016/j.jsb.2015.05.007 · External reference
10.1016/j.jsb.2021.107702
10.1016/j.jsb.2021.107702 · External reference
10.1073/pnas.2419140122
10.1073/pnas.2419140122 · External reference
3dflex: determining structure and motion of flexible proteins from cryo-em
10.1038/s41592-023-01853-8 · 2023 · External reference
Dynamight: estimating molecular motions with improved reconstruction from cryo-em images
10.1038/s41592-024-02377-5 · 2024 · External reference
Cryostar: leveraging structural priors and constraints for cryo-em heterogeneous reconstruction
10.1038/s41592-024-02486-1 · 2024 · External reference
10.1016/j.jsb.2013.10.006
10.1016/j.jsb.2013.10.006 · External reference
10.1016/j.cpc.2016.09.014
10.1016/j.cpc.2016.09.014 · External reference
A bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments
10.1038/s41598-021-92621-1 · 2021 · External reference
Ensemble reweighting using cryo-em particle images
10.1021/acs.jpcb.3c01087 · 2023 · External reference
10.1073/pnas.2420158122
10.1073/pnas.2420158122 · External reference
10.1126/sciadv.1501177
10.1126/sciadv.1501177 · External reference
Simultaneous determination of protein structure and dynamics using cryo-electron microscopy
10.1016/j.bpj.2018.02.028 · 2018 · External reference
Determination of intermediate state structures in the opening pathway of sars-cov-2 spike using cryo-electron microscopy
10.1039/d1sc00244a · 2021 · External reference
Ensemble refinement of mismodeled cryo-em rna structures using all-atom simulations
10.1038/s41467-025-59769-0 · 2025 · External reference
Cryo-electron microscopy structural ensemble optimization using individual particles
10.1021/acs.jctc.6c00053 · 2026 · External reference
Cryobench: Diverse and challenging datasets for the heterogeneity problem in cryo-em
2024 · External reference
10.1038/s41467-025-67821-2
10.1038/s41467-025-67821-2 · External reference
10.1101/2025.07.18.665582
10.1101/2025.07.18.665582 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
10.7554/elife.75751
10.7554/elife.75751 · External reference
10.1016/j.sbi.2026.103253
10.1016/j.sbi.2026.103253 · External reference
10.1063/1.4937786
10.1063/1.4937786 · External reference
Exendiff: an experiment-guided diffusion model for protein conformational ensemble generation
10.1103/prxlife.3.023013 · 2025 · External reference
Simulation-driven design of stabilized sars-cov-2 spike s2 immunogens
10.1038/s41467-024-50976-9 · 2024 · External reference
Unresolved reference
External reference
A minimal, adaptive binning scheme for weighted ensemble simulations
10.1021/acs.jpca.0c10724 · 2021 · External reference
10.1016/j.bpj.2011.03.051
10.1016/j.bpj.2011.03.051 · External reference
10.1073/pnas.1800690115
10.1073/pnas.1800690115 · External reference
The role of force fields and water models in protein folding and unfolding dynamics
10.1021/acs.jctc.3c01106 · 2024 · External reference
Equilibrium sampling in biomolecular simulations
10.1146/annurev-biophys-042910-155255 · 2011 · External reference
10.1016/s1574-1400(09)00502-7
10.1016/s1574-1400(09)00502-7 · External reference
10.1007/978-1-4939-1465-4_8
10.1007/978-1-4939-1465-4_8 · External reference
Overcoming sampling issues and improving computational efficiency in collective-variable-based enhanced-sampling simulations: A tutorial
10.1021/acs.jpcb.4c04857 · 2024 · External reference
10.1038/s42254-020-0153-0
10.1038/s42254-020-0153-0 · External reference
10.1006/jsbi.1998.4014
10.1006/jsbi.1998.4014 · External reference
Counting particles in cryo-electron microscopy may result in incorrect population estimates
10.1038/s42003-026-09859-6 · 2026 · External reference
Openmm 8: molecular dynamics simulation with machine learning potentials
2023 · External reference
10.1021/acs.jctc.5b00255
10.1021/acs.jctc.5b00255 · External reference
10.1063/1.445869
10.1063/1.445869 · External reference
10.1063/1.470117
10.1063/1.470117 · External reference
Exploring protein native states and large-scale conformational changes with a modified generalized born model
10.1002/prot.20033 · 2004 · External reference
Westpa 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications
10.1021/acs.jctc.1c01154 · 2022 · External reference
10.1016/j.str.2004.05.022
10.1016/j.str.2004.05.022 · External reference
10.1021/ja8030533
10.1021/ja8030533 · External reference
10.1016/j.febslet.2006.05.015
10.1016/j.febslet.2006.05.015 · External reference
10.1103/physrevlett.96.238102
10.1103/physrevlett.96.238102 · External reference
Oneopes, a combined enhanced sampling method to rule them all
10.1021/acs.jctc.3c00254 · 2023 · External reference
10.1073/pnas.1519712113
10.1073/pnas.1519712113 · External reference
Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation
10.1021/acs.jctc.5b00436 · 2015 · External reference
Top-down machine learning of coarse-grained protein force fields
10.1021/acs.jctc.3c00638 · 2023 · External reference
Navigating protein landscapes with a machine-learned transferable coarsegrained model
10.1038/s41557-025-01874-0 · 2025 · External reference
Aimd-chig: Exploring the conformational space of a 166-atom protein chignolin with ab initio molecular dynamics
10.1038/s41597-023-02465-9 · 2023 · External reference
Predicting residue cooperativity during protein folding: A combined, molecular dynamics and unsupervised learning approach
10.1063/5.0140113 · 2023 · External reference
Charmm36m: an improved force field for folded and intrinsically disordered proteins
10.1038/nmeth.4067 · 2017 · External reference
10.1016/j.bpj.2012.03.024
10.1016/j.bpj.2012.03.024 · External reference
10.1021/bi972352x
10.1021/bi972352x · External reference
10.1016/s0022-2836(03)00028-7
10.1016/s0022-2836(03)00028-7 · External reference
10.1021/ja9090353
10.1021/ja9090353 · External reference
The n-terminal domain of ribosomal protein l9 folds via a diffuse and delocalized transition state
10.1016/j.bpj.2017.01.034 · 2017 · External reference
Improvements in markov state model construction reveal many non-native interactions in the folding of ntl9
10.1021/ct300878a · 2013 · External reference
Vampnets for deep learning of molecular kinetics
10.1038/s41467-017-02388-1 · 2018 · External reference
Adenylate kinase and amp signaling networks: metabolic monitoring, signal communication and body energy sensing
10.3390/ijms10041729 · 2009 · External reference
10.1016/j.jmb.2009.09.009
10.1016/j.jmb.2009.09.009 · External reference
10.1073/pnas.0706443104
10.1073/pnas.0706443104 · External reference
Path similarity analysis: a method for quantifying macromolecular pathways
10.1371/journal.pcbi.1004568 · 2015 · External reference
10.1016/j.jmb.2006.11.085
10.1016/j.jmb.2006.11.085 · External reference
10.1038/nature06410
10.1038/nature06410 · External reference
10.1016/0022-2836(92)90582-5
10.1016/0022-2836(92)90582-5 · External reference
10.1016/s0969-2126(96)00018-4
10.1016/s0969-2126(96)00018-4 · External reference
10.1371/journal.pone.0004203
10.1371/journal.pone.0004203 · External reference
Rethinking the effective sample size
10.1111/insr.12500 · 2022 · External reference
10.1063/1.3565032
10.1063/1.3565032 · External reference
10.1137/070699500
10.1137/070699500 · External reference
Efficient ensemble refinement by reweighting
10.1021/acs.jctc.8b01231 · 2019 · External reference
10.1016/j.sbi.2016.12.004
10.1016/j.sbi.2016.12.004 · External reference
10.3390/molecules180910548
10.3390/molecules180910548 · External reference
Bayesian refinement of protein structures and nsembles against saxs data using molecular dynamics
10.1371/journal.pcbi.1005800 · 2017 · External reference
Combining molecular dynamics simulations with small-angle x-ray and neutron scattering data to study multi-domain proteins in solution
10.1371/journal.pcbi.1007870 · 2020 · External reference
10.1073/pnas.202427399
10.1073/pnas.202427399 · External reference
10.1002/wcms.31
10.1002/wcms.31 · External reference
New advances in metadynamics
2012 · External reference
10.1063/1.1738640
10.1063/1.1738640 · External reference
Milestoning: An efficient approach for atomically detailed simulations of kinetics in biophysics
10.1146/annurev-biophys-121219-081528 · 2020 · External reference
Advances and challenges in milestoning simulations for drug–target kinetics
10.1021/acs.jctc.4c01108 · 2024 · External reference
10.1021/acs.jcim.2c00501
10.1021/acs.jcim.2c00501 · External reference
10.1007/978-3-642-58360-5_2
10.1007/978-3-642-58360-5_2 · External reference
10.1063/1.1651473
10.1063/1.1651473 · External reference
10.1101/2024.10.18.619077
10.1101/2024.10.18.619077 · External reference
10.1101/2025.10.23.682564
10.1101/2025.10.23.682564 · External reference
10.1016/j.bpj.2013.03.032
10.1016/j.bpj.2013.03.032 · External reference
Dynamic Model Exposes the Energetics and Dynamics of the Injection Machinery for Bacteriophage T4
10.1016/j.bpj.2017.05.029 · 2017 · External reference
A First Model of the Dynamics of the Bacteriophage T4 Injection Machinery
10.1115/1.4033554 · 2016 · External reference
10.1073/pnas.1909298116
10.1073/pnas.1909298116 · External reference
