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Quantitative reactivity profiling predicts functional cysteines in proteomes
Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines… Expand
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
RosettaScripts is an XML-like language for specifying modeling tasks in the Rosetta framework that provides access to a wide range of modeling capabilities. Expand
Computational design of ligand-binding proteins with high affinity and selectivity
The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Expand
De Novo Enzyme Design Using Rosetta3
The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of… Expand
Structure prediction for CASP7 targets using extensive all‐atom refinement with Rosetta@home
We describe predictions made using the Rosetta structure prediction methodology for both template‐based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. Expand
Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases
- S. Khare, F. Ding, Kenneth N. Gwanmesia, N. Dokholyan
- Biology, Medicine
- PLoS Comput. Biol.
- 1 August 2005
We show that a mechanism of aggregation is the conformational transition in a single polyQ peptide chain from random coil to a parallel β-helix. Expand
The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide dismutase in amyotrophic lateral sclerosis.
- S. Khare, M. Caplow, N. Dokholyan
- Medicine, Chemistry
- Proceedings of the National Academy of Sciences…
- 19 October 2004
Mutation-induced aggregation of the dimeric enzyme Cu, Zn superoxide dismutase 1 (SOD1) has been implicated in the familial form of the disease amyotrophic lateral sclerosis, but the mechanism of… Expand
Can contact potentials reliably predict stability of proteins?
- Jainab Khatun, S. Khare, N. Dokholyan
- Chemistry, Medicine
- Journal of molecular biology
- 19 February 2004
The simplest approximation of interaction potential between amino acid residues in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of… Expand
Engineering V-type nerve agents detoxifying enzymes using computationally focused libraries.
- Izhack Cherny, Per Greisen, +5 authors Dan S. Tawfik
- Chemistry, Medicine
- ACS chemical biology
- 4 October 2013
VX and its Russian (RVX) and Chinese (CVX) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. These organophosphates have a thiol leaving group with a… Expand
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate.
Mounting evidence suggests that the focal adhesion targeting (FAT) domain, an antiparallel four-helix bundle, exists in alternative conformations that may modulate phosphorylation, ligand binding,… Expand