Euclidean sections of protein conformation space and their implications in dimensionality reduction

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Euclidean sections of protein conformation space and their implications in dimensionality reduction is …
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scholarly articleQ13442814

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P356DOI10.1002/PROT.24622
P932PMC publication ID4177328
P698PubMed publication ID24913095
P5875ResearchGate publication ID262978627

P2093author name stringLi Han
Shuanghong Huo
Mojie Duan
Minghai Li
P2860cites workCHARMM: the biomolecular simulation programQ24658108
UCSF Chimera--a visualization system for exploratory research and analysisQ27860666
Effective energy function for proteins in solutionQ28142746
Calculation of the free energy and cooperativity of protein foldingQ28469199
Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.Q30990030
Algorithmic dimensionality reduction for molecular structure analysisQ33603623
Domain communication in the dynamical structure of human immunodeficiency virus 1 proteaseQ33894965
Nonlinear dimensionality reduction by locally linear embeddingQ33928873
An experimental and computational investigation of spontaneous lasso formation in microcin J25.Q34250528
Initial conformational changes of human transthyretin under partially denaturing conditionsQ34350522
Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.Q34481107
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reductionQ34772955
Network and graph analyses of folding free energy surfacesQ36368757
Evaluation of Dimensionality-Reduction Methods from Peptide Folding–Unfolding SimulationsQ36919267
Graph representation of protein free energy landscapeQ37350472
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptidesQ37480652
Hidden complexity of free energy surfaces for peptide (protein) foldingQ37571434
MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond ScaleQ39373045
A global geometric framework for nonlinear dimensionality reductionQ47014659
Structural and pathway complexity of beta-strand reorganization within aggregates of human transthyretin(105-115) peptideQ51917333
Global optimization and folding pathways of selected alpha-helical proteinsQ51956530
Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulationsQ52465150
Archetypal energy landscapesQ59065364
Large-amplitude nonlinear motions in proteinsQ74514543
The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretinQ79141191
Evaluation of configurational entropy methods from peptide folding-unfolding simulationQ79895609
P433issue10
P407language of work or nameEnglishQ1860
P921main subjectdimensionality reductionQ16000077
P304page(s)2585-2596
P577publication date2014-06-19
P1433published inProteinsQ7251514
P1476titleEuclidean sections of protein conformation space and their implications in dimensionality reduction
P478volume82

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cites work (P2860)
Q90106735Approximating dynamic proximity with a hybrid geometry energy-based kernel for diffusion maps
Q39204260Charting molecular free-energy landscapes with an atlas of collective variables.
Q59122842Energy Landscape of Pentapeptides in a Higher-Order (ϕ,ψ) Conformational Subspace
Q30886821Topological obstructions in the way of data-driven collective variables

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