Topological obstructions in the way of data-driven collective variables

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

(2014) Mojie Duan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

(2013) Behrooz Hashemian et al.   JOURNAL OF CHEMICAL PHYSICS

Demonstrating the Transferability and the Descriptive Power of Sketch-Map

(2013) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Variation of conformational properties at a glance. True graphical visualization of the Ramachandran surface topology as a periodic potential energy surface

(2012) Imre Jákli et al.   CHEMICAL PHYSICS LETTERS

State reduction in molecular simulations

(2012) Yuzhen Xue et al.   COMPUTERS & CHEMICAL ENGINEERING

Molecular Dynamics in Principal Component Space

(2012) Servaas Michielssens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

(2012) G. A. Tribello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide

(2011) Andrew L. Ferguson et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

(2011) Vojtěch Spiwok et al.   JOURNAL OF CHEMICAL PHYSICS

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

(2011) Michele Ceriotti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topology of cyclo-octane energy landscape

(2010) Shawn Martin et al.   JOURNAL OF CHEMICAL PHYSICS

Metadynamics convergence law in a multidimensional system

(2010) Yanier Crespo et al.   PHYSICAL REVIEW E

Systematic determination of order parameters for chain dynamics using diffusion maps

(2010) A. L. Ferguson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1

(2009) Fabio Pietrucci et al.   Journal of Chemical Theory and Computation

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

(2009) Hernán Stamati et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Algorithmic dimensionality reduction for molecular structure analysis

(2008) W. Michael Brown et al.   JOURNAL OF CHEMICAL PHYSICS

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

Advillin Folding Takes Place on a Hypersurface of Small Dimensionality

(2008) Stefano Piana et al.   PHYSICAL REVIEW LETTERS