Unsupervised learning methods for molecular simulation data
Unsupervised learning is becoming an essential tool to analyze the increasingly large
amounts of data produced by atomistic and molecular simulations, in material science, solid …
amounts of data produced by atomistic and molecular simulations, in material science, solid …
The role of protein loops and linkers in conformational dynamics and allostery
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …
take place on a wide range of time scales. These changes can be as small as the rotation of …
PyEMMA 2: A software package for estimation, validation, and analysis of Markov models
MK Scherer, B Trendelkamp-Schroer… - Journal of chemical …, 2015 - ACS Publications
Markov (state) models (MSMs) and related models of molecular kinetics have recently
received a surge of interest as they can systematically reconcile simulation data from either …
received a surge of interest as they can systematically reconcile simulation data from either …
Protein allostery and conformational dynamics
The functions of many proteins are regulated through allostery, whereby effector binding at a
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …
Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …
Markov state models to study the functional dynamics of proteins in the wake of machine learning
Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …
employed to study protein folding, however, their application to functional conformational …
Emerging computational methods for the rational discovery of allosteric drugs
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …
An efficient path classification algorithm based on variational autoencoder to identify metastable path channels for complex conformational changes
Conformational changes (ie, dynamic transitions between pairs of conformational states)
play important roles in many chemical and biological processes. Constructing the Markov …
play important roles in many chemical and biological processes. Constructing the Markov …
Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
RE Amaro, AJ Mulholland - Nature Reviews Chemistry, 2018 - nature.com
Drug action is inherently multiscale: it connects molecular interactions to emergent
properties at cellular and larger scales. Simulation techniques at each of these different …
properties at cellular and larger scales. Simulation techniques at each of these different …
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
The function of complex biomolecular machines relies heavily on their conformational
changes. Investigating these functional conformational changes is therefore essential for …
changes. Investigating these functional conformational changes is therefore essential for …