Distance geometry and protein loop modeling
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DOI: 10.1002/jcc.26796
Abstract: Due to the role of loops in protein function, loop modeling is an important problem in computational biology. We present a new approach to loop modeling based on a combinatorial version of distance geometry, where… read more here.
Keywords: protein loop; geometry; loop modeling; geometry protein ... See more keywords
Clifford algebra and discretizable distance geometry
Sign Up to like & getrecommendations! Published in 2018 at "Mathematical Methods in The Applied Sciences"
DOI: 10.1002/mma.4422
Abstract: Protein structure calculations using nuclear magnetic resonance (NMR) experiments are one of the most important applications of distance geometry. The chemistry of proteins and the NMR data allow us to define an atomic order, such… read more here.
Keywords: discretizable distance; geometry; distance geometry; clifford algebra ... See more keywords
Geometric Algebra to Describe the Exact Discretizable Molecular Distance Geometry Problem for an Arbitrary Dimension
Sign Up to like & getrecommendations! Published in 2019 at "Advances in Applied Clifford Algebras"
DOI: 10.1007/s00006-019-0995-7
Abstract: The K-Discretizable Molecular Distance Geometry Problem ( $$^{\textit{K}}\hbox {DMDGP}$$ ) is a subclass of the Distance Geometry Problem (DGP), whose complexity is NP-hard, such that the search space is finite. In this work, the authors describe… read more here.
Keywords: distance geometry; geometry problem; discretizable molecular; geometry ... See more keywords
Preface: Special issue dedicated to Distance Geometry
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DOI: 10.1007/s10898-018-0693-3
Abstract: This preface introduces the special issue of the Journal of Global Optimization dedicated to the workshop “Distance Geometry Theory and Applications” (DGTA16) which took place at the DIMACS Center, Rutgers University, Piscataway NJ, USA. read more here.
Keywords: special issue; preface; geometry; distance geometry ... See more keywords
Unassigned distance geometry and molecular conformation problems
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DOI: 10.1007/s10898-021-01023-0
Abstract: 3D protein structures and nanostructures can be obtained by exploiting distance information provided by experimental techniques, such as nuclear magnetic resonance and the pair distribution function method. These are examples of instances of the unassigned… read more here.
Keywords: distance; geometry molecular; geometry; unassigned distance ... See more keywords
Rejoinder on: Distance geometry and data science
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DOI: 10.1007/s11750-020-00564-z
Abstract: The invited surveys at TOP are routinely assigned to three reviewers, who write public (and signed) reports. The author of the survey is then given the opportunity of a rebuttal. read more here.
Keywords: rejoinder distance; data science; geometry data; geometry ... See more keywords
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c00025
Abstract: The conformer generator ETKDG is a stochastic search method that utilises distance geometry together with knowledge derived from experimental crystal structures. It has been shown to generate good conformers for acyclic, flexible molecules. This work… read more here.
Keywords: conformer; geometry; distance geometry; conformer generation ... See more keywords
Incorporating NOE-Derived Distances in Conformer Generation of Cyclic Peptides with Distance Geometry
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DOI: 10.1021/acs.jcim.1c01165
Abstract: Nuclear magnetic resonance (NMR) data from NOESY (nuclear Overhauser enhancement spectroscopy) and ROESY (rotating frame Overhauser enhancement spectroscopy) experiments can easily be combined with distance geometry (DG) based conformer generators by modifying the molecular distance… read more here.
Keywords: geometry; cyclic peptides; spectroscopy; distance geometry ... See more keywords
Systematic exploration of protein conformational space using a Distance Geometry approach.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.9b00215
Abstract: The optimisation approaches classically used during the determination of protein structure encounter various diffculties, specially when the size of the conformational space is large. Indeed, in such case, algorithmic convergence criteria are more difficult to… read more here.
Keywords: geometry; distance geometry; conformational space; approach ... See more keywords
Bayesian Inference Applied to NMR-Based Configurational Assignments by Floating Chirality Distance Geometry Calculations.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of the American Chemical Society"
DOI: 10.1021/jacs.2c00813
Abstract: Using NMR data, the assignment of the correct 3D configuration and conformation to unknown natural products is of pivotal importance in pharmaceutical and medicinal chemistry. In this report, we quantify the quality and probability of… read more here.
Keywords: bayesian inference; floating chirality; geometry; chirality distance ... See more keywords