Conformational Sampling for Transition State Searches on a Computational Budget.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00081
Abstract: Transition state searches are the basis for computationally characterizing reaction mechanisms, making them a pivotal tool in myriad chemical applications. Nevertheless, common search algorithms are sensitive to reaction conformations, and the conformational spaces of even… read more here.
Keywords: conformational sampling; transition state; reaction; state searches ... See more keywords
The impact of conformational sampling on first-principles calculations of vicinal COCH J-couplings in carbohydrates.
Sign Up to like & getrecommendations! Published in 2022 at "Glycobiology"
DOI: 10.1093/glycob/cwac073
Abstract: Dihedral angles in organic molecules and biomolecules are vital structural parameters that can be indirectly probed by NMR measurements of vicinal J-couplings. The empirical relations that map the measured couplings to dihedral angles are typically… read more here.
Keywords: principles calculations; impact conformational; sampling first; first principles ... See more keywords
Conformational Sampling of a Biomolecular Rugged Energy Landscape
Sign Up to like & getrecommendations! Published in 2018 at "IEEE/ACM Transactions on Computational Biology and Bioinformatics"
DOI: 10.1109/tcbb.2016.2634008
Abstract: The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper, we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of… read more here.
Keywords: potential energy; energy landscape; energy; conformational sampling ... See more keywords
Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins
Sign Up to like & getrecommendations! Published in 2018 at "Bulletin of the Chemical Society of Japan"
DOI: 10.1246/bcsj.20180170
Abstract: The biological functions of proteins are strongly related to their conformational transitions. To elucidate the essential dynamics, molecular dynamics (MD) simulation has become a powerful tool. However, it might still be difficult to address the… read more here.
Keywords: sampling methods; rare events; conformational sampling; conformational transitions ... See more keywords
How Does the Number of Initial Structures Affect the Conformational Sampling Efficiency and Quality in Parallel Cascade Selection Molecular Dynamics (PaCS-MD)?
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DOI: 10.1246/cl.170207
Abstract: The Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is an enhanced conformational sampling to promote structural transitions from a given reactant. We here assessed how a number of initial structures, ninitial, affected the conformational sampling efficiency.… read more here.
Keywords: sampling; sampling efficiency; conformational sampling; cascade selection ... See more keywords
Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function
Sign Up to like & getrecommendations! Published in 2018 at "PLoS ONE"
DOI: 10.1371/journal.pone.0207899
Abstract: In the histidine kinase family, the HAMP and DHp domains are considered to play an important role into the transmission of signal arising from environmental conditions to the auto-phosphorylation site and to the binding site… read more here.
Keywords: sampling cpxa; histidine kinase; cpxa connecting; hamp motions ... See more keywords
Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank
Sign Up to like & getrecommendations! Published in 2018 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms19113405
Abstract: In this article, we present a method for the enhanced molecular dynamics simulation of protein and DNA systems called potential of mean force (PMF)-enriched sampling. The method uses partitions derived from the potentials of mean… read more here.
Keywords: protein; data bank; hybrid hamiltonian; method ... See more keywords
Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder
Sign Up to like & getrecommendations! Published in 2023 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms24086896
Abstract: Intrinsically disordered proteins (IDPs) account for more than 50% of the human proteome and are closely associated with tumors, cardiovascular diseases, and neurodegeneration, which have no fixed three-dimensional structure under physiological conditions. Due to the… read more here.
Keywords: sampling intrinsically; disordered ordered; intrinsically disordered; autoencoder ... See more keywords