Principal component analysis and related methods for investigating the dynamics of biological macromolecules
A Kitao - J, 2022 - mdpi.com
Principal component analysis (PCA) is used to reduce the dimensionalities of high-
dimensional datasets in a variety of research areas. For example, biological …
dimensional datasets in a variety of research areas. For example, biological …
On the uses of PCA to characterise molecular dynamics simulations of biological macromolecules: basics and tips for an effective use
J Palma, G Pierdominici‐Sottile - ChemPhysChem, 2023 - Wiley Online Library
Abstract Principal Component Analysis (PCA) is a procedure widely used to examine data
collected from molecular dynamics simulations of biological macromolecules. It allows for …
collected from molecular dynamics simulations of biological macromolecules. It allows for …
[HTML][HTML] A potential CSH nucleation mechanism: atomistic simulations of the portlandite to CSH transformation
The nucleation of the CSH gel is a complex process, key to controlling the hydration kinetics
and microstructure development of cement. In this paper, a mechanism for the crystallization …
and microstructure development of cement. In this paper, a mechanism for the crystallization …
Anisotropic friction in a ligand-protein complex
The effect of an externally applied directional force on molecular friction is so far poorly
understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin …
understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin …
Multisecond ligand dissociation dynamics from atomistic simulations
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in
order to allow the description of processes occurring on biologically relevant timescales. For …
order to allow the description of processes occurring on biologically relevant timescales. For …
Differentiable molecular simulations for control and learning
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable
both the elucidation of fundamental mechanisms and the engineering of matter for desired …
both the elucidation of fundamental mechanisms and the engineering of matter for desired …
A review on description dynamics and conformational changes of proteins using combination of principal component analysis and molecular dynamics simulation
S Moradi, A Nowroozi, MA Nezhad, P Jalali… - Computers in Biology …, 2024 - Elsevier
Understanding how proteins behave dynamically and undergo conformational changes is
essential to comprehending their biological roles. This review article examines the potent …
essential to comprehending their biological roles. This review article examines the potent …
Investigation of rare protein conformational transitions via dissipation-corrected targeted molecular dynamics
To sample rare events, dissipation-corrected targeted molecular dynamics (dcTMD) applies
a constant velocity constraint along a one-dimensional reaction coordinate s, which drives …
a constant velocity constraint along a one-dimensional reaction coordinate s, which drives …
Ligand unbinding pathway and mechanism analysis assisted by machine learning and graph methods
We present two methods to reveal protein–ligand unbinding mechanisms in biased
unbinding simulations by clustering trajectories into ensembles representing unbinding …
unbinding simulations by clustering trajectories into ensembles representing unbinding …
Repurposing of Drug Bank Compounds against Plasmodium falciparum Dihydroorotate Dehydrogenase as novel anti malarial drug candidates by Computational …
This study aimed to repurpose Drug Bank Compounds against P. falciparum Dihydroorotate
dehydrogenase (Pf-DHODH) a potential molecular target for antimalarial drug development …
dehydrogenase (Pf-DHODH) a potential molecular target for antimalarial drug development …