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Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro
The dengue protease NS2B/NS3pro has been reported to adopt either an ‘open’ or a ‘closed’ conformation. We have developed a conformational filter...
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Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties
Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative...
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Monte Carlo Approaches to Study Protein Conformation Ensembles
The molecular dynamics (MD) simulation method is widely used to determine the protein folding sampling by applying various force fields. The results...
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Functional Ensembles in the Brains of Humans and Animals
AbstractThis paper discusses the formation of functional ensembles in the brain. On the basis of recent data, it is concluded that neuronal ensembles...
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Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN
Single-particle cryogenic electron microscopy (cryo-EM) has emerged as a powerful technique to visualize the structural landscape sampled by a...
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Models of Joint Distribution of Species on the Example of Benthic Communities from Small Rivers of the Volga Basin
Abstract —The theoretical and practical aspects of building of joint species-distribution models, a modern tool for the analysis of ecological...
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Single-cell subcellular protein localisation using novel ensembles of diverse deep architectures
Unravelling protein distributions within individual cells is vital to understanding their function and state and indispensable to develo** new...
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Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their...
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Creating Computational Models of Ion Channel Dynamics
Markov models are widely used to represent ion channel protein configurations as different states in the model’s topology. Such models allow for...
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Small-Angle X-Ray Scattering for Macromolecular Complexes
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their...
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Proposal and extensive test of a calibration protocol for crop phenology models
A major effect of environment on crops is through crop phenology, and therefore, the capacity to predict phenology for new environments is important....
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A quantitative model of ensemble perception as summed activation in feature space
Ensemble perception is a process by which we summarize complex scenes. Despite the importance of ensemble perception to everyday cognition, there are...
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Conformational ensemble-dependent lipid recognition and segregation by prenylated intrinsically disordered regions in small GTPases
We studied diverse prenylated intrinsically disordered regions (PIDRs) of Ras and Rho family small GTPases using long timescale atomistic molecular...
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KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion
Ribosome assembly is orchestrated by many assembly factors, including ribosomal RNA methyltransferases, whose precise role is poorly understood....
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Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various...
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Connected impacts: combining migration tracking data with species distribution models reveals the complex potential impacts of climate change on European bee-eaters
Climate change is a key driver of biodiversity loss in multiple ecosystems, which can act at multiple stages of a species life- and annual cycle....
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Ensemble of models shows coherent response of a reservoir’s stratification and ice cover to climate warming
Water temperature, ice cover, and lake stratification are important physical properties of lakes and reservoirs that control mixing as well as...
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Spatial Models of Piezo Proteins and Protein‒Protein Interaction Networks in Trichoplax Animals (Placozoa)
AbstractThe marine free-living organism Trichoplax (phylum Placozoa) resembles a unicellular amoeba in shape and type of movement. Trichoplax ...
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Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae
The paper presents the results of recent work at the Department of Biophysics of the Biological Faculty, Lomonosov Moscow State University on the...
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Consensus clustering for Bayesian mixture models
BackgroundCluster analysis is an integral part of precision medicine and systems biology, used to define groups of patients or biomolecules....
