On the binding affinity of macromolecular interactions: daring to ask why proteins interact
PL Kastritis, AMJJ Bonvin - Journal of The Royal Society …, 2013 - royalsocietypublishing.org
Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …
underlying cellular function. The binding affinity, defined as the strength of these …
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 …
FATCAT 2.0: towards a better understanding of the structural diversity of proteins
Abstract FATCAT 2.0 server (http://fatcat. godziklab. org/), provides access to a flexible
protein structure alignment algorithm developed in our group. In such an alignment …
protein structure alignment algorithm developed in our group. In such an alignment …
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …
how macromolecules carry out their functions in the cell. Significant advances have been …
Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier
L Orellana - Frontiers in molecular biosciences, 2019 - frontiersin.org
Large-scale conformational changes are essential to link protein structures with their
function at the cell and organism scale, but have been elusive both experimentally and …
function at the cell and organism scale, but have been elusive both experimentally and …
iMod: multipurpose normal mode analysis in internal coordinates
Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …
are critical for understanding macromolecular functioning. Coarse-grained representations …
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 …
Millisecond dynamics of RNA polymerase II translocation at atomic resolution
Transcription is a central step in gene expression, in which the DNA template is processively
read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA …
read by RNA polymerase II (Pol II), synthesizing a complementary messenger RNA …
Birth and future of multiscale modeling for macromolecular systems (Nobel Lecture)
M Levitt - Angewandte Chemie International Edition, 2014 - Wiley Online Library
Winning the Nobel Prize is a unique and marvelous experience that no one can prepare for
or in any way know what to expect. The instantaneous transformation from an ordinary …
or in any way know what to expect. The instantaneous transformation from an ordinary …
In silico identification of a β2-adrenoceptor allosteric site that selectively augments canonical β2AR-Gs signaling and function
Activation of β2-adrenoceptors (β2ARs) causes airway smooth muscle (ASM) relaxation and
bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and …
bronchodilation, and β2AR agonists (β-agonists) are front-line treatments for asthma and …