Structure-guided protein transition modeling with a probabilistic roadmap algorithm
Proteins are macromolecules in perpetual motion, switching between structural states to
modulate their function. A detailed characterization of the precise yet complex relationship …
modulate their function. A detailed characterization of the precise yet complex relationship …
Computing energy landscape maps and structural excursions of proteins
Background Structural excursions of a protein at equilibrium are key to biomolecular
recognition and function modulation. Protein modeling research is driven by the need to aid …
recognition and function modulation. Protein modeling research is driven by the need to aid …
Reducing ensembles of protein tertiary structures generated de novo via clustering
Controlling the quality of tertiary structures computed for a protein molecule remains a
central challenge in de-novo protein structure prediction. The rule of thumb is to generate as …
central challenge in de-novo protein structure prediction. The rule of thumb is to generate as …
Sample-based models of protein energy landscapes and slow structural rearrangements
T Maximova, Z Zhang, DB Carr, E Plaku… - Journal of …, 2018 - liebertpub.com
Proteins often undergo slow structural rearrangements that involve several angstroms and
surpass the nanosecond timescale. These spatiotemporal scales challenge physics-based …
surpass the nanosecond timescale. These spatiotemporal scales challenge physics-based …
A survey of computational treatments of biomolecules by robotics-inspired methods modeling equilibrium structure and dynamic
More than fifty years of research in molecular biology have demonstrated that the ability of
small and large molecules to interact with one another and propagate the cellular processes …
small and large molecules to interact with one another and propagate the cellular processes …
Sample-based models of protein structural transitions
Modeling structural transitions of a protein at equilibrium is central to understanding function
modulation but challenging due to the disparate spatio-temporal scales involved. Of …
modulation but challenging due to the disparate spatio-temporal scales involved. Of …
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling
We have long known that characterizing protein structures structure is key to understanding
protein function. Computational approaches have largely addressed a narrow formulation of …
protein function. Computational approaches have largely addressed a narrow formulation of …
Efficient exploration of protein conformational pathways using rrt* and mc
F Afrasiabi, N Haspel - Proceedings of the 11th ACM International …, 2020 - dl.acm.org
The conformational space of proteins is complex and high dimensional, which makes its
analysis a highly challenging task. Understanding the structure and dynamics of proteins is …
analysis a highly challenging task. Understanding the structure and dynamics of proteins is …
Integrating rigidity analysis into the exploration of protein conformational pathways using rrt* and mc
To understand how proteins function on a cellular level, it is of paramount importance to
understand their structures and dynamics, including the conformational changes they …
understand their structures and dynamics, including the conformational changes they …
Integrating co-evolutionary information in monte carlo based method for proteins trajectory simulation
The conformational space of proteins is complex and high dimensional, which makes its
analysis a highly challenging task. Understanding the structure and dynamics of proteins is …
analysis a highly challenging task. Understanding the structure and dynamics of proteins is …