Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …
Global dynamics of proteins: bridging between structure and function
Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …
their biological functions. Recent studies indicate that these dynamic properties are …
Principal component analysis: a method for determining the essential dynamics of proteins
CC David, DJ Jacobs - Protein dynamics: Methods and protocols, 2014 - Springer
It has become commonplace to employ principal component analysis to reveal the most
important motions in proteins. This method is more commonly known by its acronym, PCA …
important motions in proteins. This method is more commonly known by its acronym, PCA …
ProDy: Protein Dynamics Inferred from Theory and Experiments
We developed a Python package, ProDy, for structure-based analysis of protein dynamics.
ProDy allows for quantitative characterization of structural variations in heterogeneous …
ProDy allows for quantitative characterization of structural variations in heterogeneous …
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
The conformational flexibility of target proteins continues to be a major challenge in accurate
modeling of protein–inhibitor interactions. A fundamental issue, yet to be clarified, is whether …
modeling of protein–inhibitor interactions. A fundamental issue, yet to be clarified, is whether …
Structural and dynamic characterizations highlight the deleterious role of SULT1A1 R213H polymorphism in substrate binding
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous
and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 …
and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 …
Adaptability of protein structures to enable functional interactions and evolutionary implications
T Haliloglu, I Bahar - Current opinion in structural biology, 2015 - Elsevier
Highlights•Intrinsic dynamics plays a major role in enabling protein interactions.•Soft/global
modes of motions facilitate binding and assembly.•Soft modes define pre-existing pathways …
modes of motions facilitate binding and assembly.•Soft modes define pre-existing pathways …
WEBnm@ v2. 0: Web server and services for comparing protein flexibility
Background Normal mode analysis (NMA) using elastic network models is a reliable and
cost-effective computational method to characterise protein flexibility and by extension, their …
cost-effective computational method to characterise protein flexibility and by extension, their …
Multiscale methods for macromolecular simulations
In this article we review the key modeling tools available for simulating biomolecular
systems. We consider recent developments and representative applications of mixed …
systems. We consider recent developments and representative applications of mixed …
Measuring and comparing structural fluctuation patterns in large protein datasets
Motivation: The function of a protein depends not only on its structure but also on its
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …
dynamics. This is at the basis of a large body of experimental and theoretical work on protein …