User profiles for R. A. Pache
Roland PacheUCSF Verified email at ucsf.edu Cited by 961 |
Scientific benchmarks for guiding macromolecular energy function improvement
Accurate energy functions are critical to macromolecular modeling and design. We describe
new tools for identifying inaccuracies in energy functions and guiding their improvement, …
new tools for identifying inaccuracies in energy functions and guiding their improvement, …
Dynamic interactions of proteins in complex networks: a more structured view
Virtually every process in a cell is carried out by macromolecular complexes whose actions
need to be perfectly orchestrated. The synchronization and regulation of these biological …
need to be perfectly orchestrated. The synchronization and regulation of these biological …
Computational design of a modular protein sense-response system
…, AL Loshbaugh, J Pellegrino, C Krivacic, RA Pache… - Science, 2019 - science.org
Sensing and responding to signals is a fundamental ability of living systems, but despite
substantial progress in the computational design of new protein structures, there is no general …
substantial progress in the computational design of new protein structures, there is no general …
[HTML][HTML] A web resource for standardized benchmark datasets, metrics, and Rosetta protocols for macromolecular modeling and design
The development and validation of computational macromolecular modeling and design
methods depend on suitable benchmark datasets and informative metrics for comparing …
methods depend on suitable benchmark datasets and informative metrics for comparing …
Engineering a light-activated caspase-3 for precise ablation of neurons in vivo
The circuitry of the brain is characterized by cell heterogeneity, sprawling cellular anatomy,
and astonishingly complex patterns of connectivity. Determining how complex neural circuits …
and astonishingly complex patterns of connectivity. Determining how complex neural circuits …
Uncovering new substrates for Aurora A kinase
Aurora A is a serine/threonine kinase that is essential for a wide variety of cell‐cycle‐related
events, but only a small number of its substrates are known. We present and validate a …
events, but only a small number of its substrates are known. We present and validate a …
[HTML][HTML] The role of structural disorder in the rewiring of protein interactions through evolution
Structurally disordered regions play a key role in protein-protein interaction networks and
the evolution of highly connected proteins, enabling the molecular mechanisms for multiple …
the evolution of highly connected proteins, enabling the molecular mechanisms for multiple …
NetAligner—a network alignment server to compare complexes, pathways and whole interactomes
The many ongoing genome sequencing initiatives are delivering comprehensive lists of the
individual molecular components present in an organism, but these reveal little about how …
individual molecular components present in an organism, but these reveal little about how …
[HTML][HTML] A novel framework for the comparative analysis of biological networks
Genome sequencing projects provide nearly complete lists of the individual components
present in an organism, but reveal little about how they work together. Follow-up initiatives have …
present in an organism, but reveal little about how they work together. Follow-up initiatives have …
Accurate positioning of functional residues with robotics-inspired computational protein design
Proteins achieve their complex functions, such as molecular recognition with high affinity and
specificity, through intricate three-dimensional geometries in functional sites. To engineer …
specificity, through intricate three-dimensional geometries in functional sites. To engineer …