4.7 Article

Protein folding intermediates on the dimensionality reduced landscape with UMAP and native contact likelihood

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

UMAP as a Dimensionality Reduction Tool for Molecular Dynamics Simulations of Biomacromolecules: A Comparison Study

Francesco Trozzi et al.

Summary: This study compared the performance of different dimensionality reduction methods in analyzing molecular dynamics simulations of the circadian clock protein VIVID, showing that UMAP outperforms linear methods like PCA and tICA in accurately representing data structures with competitive performance and scalable computational cost.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Biochemistry & Molecular Biology

Controlling the SARS-CoV-2 spike glycoprotein conformation

Rory Henderson et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Dimensionality reduction for visualizing single-cell data using UMAP

Etienne Becht et al.

NATURE BIOTECHNOLOGY (2019)

Review Chemistry, Multidisciplinary

Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules

Wei Wang et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2018)

Review Chemistry, Multidisciplinary

Markov State Models: From an Art to a Science

Brooke E. Husic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Chemistry, Physical

t-Distributed Stochastic Neighbor Embedding Method with the Least Information Loss for Macromolecular Simulations

Hongyu Zhou et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Chemistry, Physical

Perspective: Identification of collective variables and metastable states of protein dynamics

Florian Sittel et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Multidisciplinary

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

Chigusa Kobayashi et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

Article Chemistry, Physical

Optimized parameter selection reveals trends in Markov state models for protein folding

Brooke E. Husic et al.

JOURNAL OF CHEMICAL PHYSICS (2016)

Article Chemistry, Physical

Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein

Yasuhiro Matsunaga et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)

Article Chemistry, Physical

Contact- and distance-based principal component analysis of protein dynamics

Matthias Ernst et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Variational cross-validation of slow dynamical modes in molecular kinetics

Robert T. McGibbon et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

Frank Noe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

Yinglong Miao et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

Martin K. Scherer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Multidisciplinary

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jaewoon Jung et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2015)

Article Chemistry, Physical

Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering

Abhinav Jain et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2014)

Article Chemistry, Physical

Identification of slow molecular order parameters for Markov model construction

Guillermo Perez-Hernandez et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

Christian R. Schwantes et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

Michele Ceriotti et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Multidisciplinary Sciences

Native contacts determine protein folding mechanisms in atomistic simulations

Robert B. Best et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Multidisciplinary Sciences

Simplifying the representation of complex free-energy landscapes using sketch-map

Michele Ceriotti et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Activation mechanism of the β2-adrenergic receptor

Ron O. Dror et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

How Fast-Folding Proteins Fold

Kresten Lindorff-Larsen et al.

SCIENCE (2011)

Article Multidisciplinary Sciences

Systematic determination of order parameters for chain dynamics using diffusion maps

Andrew L. Ferguson et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Multidisciplinary Sciences

Atomic-Level Characterization of the Structural Dynamics of Proteins

David E. Shaw et al.

SCIENCE (2010)

Article Chemistry, Physical

Coarse master equations for peptide folding dynamics

Nicolae-Viorel Buchete et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Multidisciplinary Sciences

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Payel Das et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps

RR Coifman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

Langevin dynamics in constant pressure extended systems

D Quigley et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biochemistry & Molecular Biology

Improved Go-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

J Karanicolas et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

The origins of asymmetry in the folding transition states of protein L and protein G

J Karanicolas et al.

PROTEIN SCIENCE (2002)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Multidisciplinary Sciences

A global geometric framework for nonlinear dimensionality reduction

JB Tenenbaum et al.

SCIENCE (2000)