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PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
SUMMARY PyRosetta is a stand-alone Python-based implementation of the Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using the majorExpand
Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
This study marks the most extensive benchmarking of the RosettaDock module to date and establishes a baseline for future research in protein interface modeling and structure prediction and quantifies the reliability of the stochastic docking results. Expand
Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking
The development and implementation of RosettaAntibody, a protocol for homology modeling of antibody variable regions, and the level of “functional accuracy” of these structural models toward protein engineering applications is revealed. Expand
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.
The marked success of CS and CS/IF docking shows that ensemble docking can be a versatile and effective method for accommodating conformational plasticity in docking and serves as a demonstration for the CS theory--that binding-competent conformers exist in the unbound ensemble and can be selected based on their favorable binding energies. Expand
Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1
A coarse-grain theoretical model of B cell affinity maturation during monovalent and polyvalent vaccinations that predicts the fine specificity and cross-reactivity of the Ab response is presented and suggests that alteredfine specificity and enhanced cross- reactivity may be a universal feature ofpolyvalent vaccines. Expand
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance.
It is shown that the very residues that are responsible for native substrate specificity in HIV-1 protease are altered during its evolution to drug resistance, suggesting that drug resistance and substrate selectivity may share common mechanisms. Expand
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12
Despite a larger number of unbound–unbound and homology model binding targets, CAPRI rounds 6–12 reinforced that RosettaDock is a powerful algorithm for predicting bound complex structures, especially when combined with experimental data Proteins 2007. Expand
Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach
The results from the ROCS-based target fishing approach are promising and have potential application in drug repurposing for single and multiple targets, identifying targets for orphan compounds, and adverse effect prediction. Expand
The biological function of antibodies induced by the RTS,S/AS01 malaria vaccine candidate is determined by their fine specificity
The findings suggest that the role of opsonization in protection in the RTS,S vaccine may be more complex than previously thought, and demonstrate how integrating multiple immune measures can provide insight into underlying mechanisms of immunity and protection. Expand
QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening
A well-validated Bayesian classification QSAR approach to rapidly screen chemical libraries for compounds predicted to have antibacterial activity is applied and suggests that a well- validation approach could compliment other screening approaches in identifying novel and promising hits. Expand