User profiles for R. A. Pache

Roland Pache

UCSF
Verified email at ucsf.edu
Cited by 961

Scientific benchmarks for guiding macromolecular energy function improvement

…, EH Kellogg, J Thompson, IW Davis, RA Pache… - Methods in …, 2013 - Elsevier
Accurate energy functions are critical to macromolecular modeling and design. We describe
new tools for identifying inaccuracies in energy functions and guiding their improvement, …

Dynamic interactions of proteins in complex networks: a more structured view

A Stein, RA Pache, P Bernado, M Pons… - The FEBS …, 2009 - Wiley Online Library
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 …

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 …

[HTML][HTML] A web resource for standardized benchmark datasets, metrics, and Rosetta protocols for macromolecular modeling and design

S ó Conchúir, KA Barlow, RA Pache, N Ollikainen… - PLOS …, 2015 - journals.plos.org
The development and validation of computational macromolecular modeling and design
methods depend on suitable benchmark datasets and informative metrics for comparing …

Engineering a light-activated caspase-3 for precise ablation of neurons in vivo

AD Smart, RA Pache, ND Thomsen… - Proceedings of the …, 2017 - National Acad Sciences
The circuitry of the brain is characterized by cell heterogeneity, sprawling cellular anatomy,
and astonishingly complex patterns of connectivity. Determining how complex neural circuits …

Uncovering new substrates for Aurora A kinase

T Sardon, RA Pache, A Stein, H Molina, I Vernos… - EMBO …, 2010 - embopress.org
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 …

[HTML][HTML] The role of structural disorder in the rewiring of protein interactions through evolution

R Mosca, RA Pache, P Aloy - Molecular & Cellular Proteomics, 2012 - ASBMB
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 …

NetAligner—a network alignment server to compare complexes, pathways and whole interactomes

RA Pache, A Céol, P Aloy - Nucleic acids research, 2012 - academic.oup.com
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 …

[HTML][HTML] A novel framework for the comparative analysis of biological networks

RA Pache, P Aloy - PloS one, 2012 - journals.plos.org
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 …

Accurate positioning of functional residues with robotics-inspired computational protein design

…, K Kundert, X Pan, RA Pache… - Proceedings of the …, 2022 - National Acad Sciences
Proteins achieve their complex functions, such as molecular recognition with high affinity and
specificity, through intricate three-dimensional geometries in functional sites. To engineer …