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SARM1 is a metabolic sensor activated by an increased NMN/NAD+ ratio to trigger axon degeneration

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Using AMBER18 for Relative Free Energy Calculations

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A gate in the selectivity filter of potassium channels

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The SARS-CoV-2 Spike variant D614G favors an open conformational state

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Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

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Molecular Dynamics Studies of Interfacial Water at the Alumina Surface

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Systematic determination of order parameters for chain dynamics using diffusion maps

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A molecular mechanism for transthyretin amyloidogenesis

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Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases

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

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Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex

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

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Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage

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Mechanistic principles underlying regulation of the actin cytoskeleton by phosphoinositides

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Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

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Insight into the Molecular Mechanisms of Protein Stabilizing Osmolytes from Global Force-Field Variations

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Machine learning prediction of antibody aggregation and viscosity for high concentration formulation development of protein therapeutics

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Structural conservation of antibiotic interaction with ribosomes

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Different positron emission tomography tau tracers bind to multiple binding sites on the tau fibril: insight from computational modeling

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Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations

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Coarse-grained modeling of polystyrene in various environments by iterative Boltzmann inversion

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Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

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Structural basis for membrane attack complex inhibition by CD59

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Two pathways mediate interdomain allosteric regulation in pin1

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Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration

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The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD

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Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

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Aspartic acid as a crystal growth catalyst

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Hypohalous Acids Contribute to Renal Extracellular Matrix Damage in Experimental Diabetes

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AlphaDesign: A de novo protein design framework based on AlphaFold

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Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney

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Allosteric inhibition of antiapoptotic MCL-1

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Enhanced EGFR Targeting Activity of Plasmonic Nanostructures with Engineered GE11 Peptide

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Ion Distribution and Hydration Structure in the Stern Layer on Muscovite Surface

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The Plasma Membrane as a Competitive Inhibitor and Positive Allosteric Modulator of KRas4B Signaling

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Gold Nanoparticle Aggregates Functionalized with Cyclic RGD Peptides for Targeting and Imaging of Colorectal Cancer Cells

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A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

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Metastable Prepores in Tension-Free Lipid Bilayers

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Structural basis for host recognition and superinfection exclusion by bacteriophage T5

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1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication

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Explore Protein Conformational Space With Variational Autoencoder

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Understanding the kinetics of barium sulfate precipitation from water and water–methanol solutions

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Predicting the Effect of a Point Mutation on a Protein Fold: The Villin and Advillin Headpieces and Their Pro62Ala Mutants

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Machine learning feature selection for predicting high concentration therapeutic antibody aggregation

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Structural and thermodynamic framework for PIEZO1 modulation by small molecules

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Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51

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Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

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Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

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Insertases scramble lipids: Molecular simulations of MTCH2

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Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

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A Diffusive Anomaly of Water in Aqueous Sodium Chloride Solutions at Low Temperatures

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A distal regulatory region of a class I human histone deacetylase

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Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore

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Molecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling

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Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds

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Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields

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Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization

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Structural pathway for PI3-kinase regulation by VPS15 in autophagy

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Autism-associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses

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New molecular-mechanics model for simulations of hydrogen fluoride in chemistry and biology

Orabi, E. A., & Faraldo-Gómez, J. D. (2020) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c00247 · Cited by 33

Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors

Dutta, S., Selvam, B., & Shukla, D. (2022) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.1c00760 · Cited by 31

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., et al. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00752 · Cited by 28

Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome

Peck Justice, S. A., Barron, M. P., Qi, G. D., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Vilseck, J. Z., Wijeratne, A. B., & Mosley, A. L. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.014576 · Cited by 28

Temperature sensitive Mutant Proteome Profiling: a novel tool for the characterization of the global impact of missense mutations on the proteome

Peck Justice, S. A., Qi, G., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Wijeratne, A. B., & Mosley, A. L. (2019) · doi:10.1101/2019.12.30.891267 · Cited by 28

Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain

Chi, G., Liang, Q., Sridhar, A., Cowgill, J. B., Sader, K., Radjainia, M., Qian, P., Castro-Hartmann, P., Venkaya, S., Singh, N. K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29594-w · Cited by 28

‘Asynchronous reciprocal coupling of Martini 2.2 coarse-grained and CHARMM36 all-atom simulations in an automated multiscale framework’

López, C. A., Zhang, X., Aydin, F., Shrestha, R., Van, Q. N., Stanley, C. B., Carpenter, T. S., Nguyen, K., Patel, L. A., Chen, D., et al. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00168 · Cited by 18

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

Wen, B., Peng, J., Zuo, X., Gong, Q., & Zhang, Z. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.07.005 · Cited by 20

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

Pfoh, R., Subramanian, A. S., Huang, J., Little, D. J., Forman, A., DiFrancesco, B. R., Balouchestani-Asli, N., Kitova, E. N., Klassen, J. S., Pomès, R., et al. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010750 · Cited by 17

Understanding the good and poor cell targeting activity of gold nanostructures functionalized with molecular units for the epidermal growth factor receptor

Mazzuca, C., Di Napoli, B., Biscaglia, F., Ripani, G., Rajendran, S., Braga, A., Benna, C., Mocellin, S., Gobbo, M., Meneghetti, M., et al. (2019) · Nanoscale Advances · doi:10.1039/c9na00096h · Cited by 16