Dynamics of folded proteins

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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Dynamic personalities of proteins

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Intrinsically disordered protein

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Atomic-level characterization of the structural dynamics of proteins

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The Protein-Folding Problem, 50 Years On

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Machine Learning Force Fields

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

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The Protein Folding Problem

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Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

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To milliseconds and beyond: challenges in the simulation of protein folding

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Millisecond-scale molecular dynamics simulations on Anton

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TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

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The future of molecular dynamics simulations in drug discovery

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Protein elastic network models and the ranges of cooperativity

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Persistent homology analysis of protein structure, flexibility, and folding

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Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity

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Exploring the role of receptor flexibility in structure-based drug discovery

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Computational studies of membrane channels

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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

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‘Scaling molecular dynamics beyond 100, 000 processor cores for large-scale biophysical simulations’

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Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Lin, Y.-S., Bowman, G. R., Beauchamp, K. A., & Pande, V. S. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2011.12.002 · Cited by 111

A topological approach for protein classification

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WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications

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Biomolecular simulation and modelling: status, progress and prospects

van der Kamp, M. W., Shaw, K. E., Woods, C. J., & Mulholland, A. J. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0105.focus · Cited by 90

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap.

Yang, Y., Lightstone, F. C., & Wong, S. E. (2013) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2013.749853 · Cited by 65

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

Periole, X. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00344 · Cited by 58

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

Allnér, O., & Nilsson, L. (2011) · RNA · doi:10.1261/rna.029231.111 · Cited by 50

Prediction of Protein B-Factor Profiles Based on Bidirectional Long Short-Term Memory Network

Wang, Q., Xiao, X., Miao, Z., Zhang, X., Yang, D., Jiang, B., & Liu, M. (2025) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbbio.2025.3564284 · Cited by 5