Karin Asensio |
Analyst |
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David Barkan |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- I am interested in improving and applying bioinformatics methods to predict protein-protein interaction specificity. I am currently predicting novel protein interaction partners in two biological systems. The first is the type three secretion system that pathogenic bacteria employ to translocate virulence proteins into host cells, and the other is with proteins involved in lymphocyte-mediated apoptotic pathways, searching for unidentified substrates of the serine protease Granzyme B.
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Ranyee Chiang |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- Evolvability of Enzyme Function - Conservation Patterns in Substrates
- Enzyme Specificity in the Enolase and Amidohydrolase Superfamilies
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David Eramian |
Graduate Student |
Graduate Program in Biophysics |
- My research aims to increase the accuracy and applicability of
computational protein models. I am addressing this goal in three
principal ways. First, I have researched and developed model
assessment scores that can identify the most native-like models from among a set of similar models and have recently developed an approach that is able to predict the accuracy of a given model in the absence of the native structure.
- Second, I have attempted to address the the primary limitation of the accuracy of comparative models--inaccuracies inherited from the alignment--by developing an iterative, genetic
algorithm-based protocol that aims to improve the accuracy of a
target/template alignment sharing low sequence identity, and the model it implies.
- Finally, I am extending the paradigm of modeling by satisfaction of
spatial restraints to include sequences with no detectable homologue of known structure.
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Hao Fan |
Postdoctoral Scholar |
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- Structure prediction on protein-ligand complex
- Small compound virtual screening using comparative models of proteins
- Structure and function prediction of amidohydrolase
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Postdoctoral Scholar |
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- assembly modeling using Small-angle X-ray scattering
- assembly modeling using cryo-electron microscopy maps
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Libusha Kelly |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- Developing a structural and evolutionary rationalization of
disease-associated and neutral point mutations in ABC transporters
- Using comparative modeling and sequence analysis.
- Profiling membrane proteins in a set of organisms representing the three major kingdoms
of life.
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Michael F. Kim |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- Developing methods for protein-protein docking using spatial restraints
from multiple data sources
- Developing methods for generalized protein assembly modeling by
hierarchical assembly
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Keren Lasker |
Junior Specialist |
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- Modeling structures of large assemblies by integrating cryo-electron microscopy data with other sources of information.
- Developing a coarse-grained optimization protocol for characterizing structures of assemblies at different levels of resolution.
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Adam C. Marko |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- Modeling of G Protein-Coupled Receptors (GPCRs)
- Development of statistical potentials for GPCR evaluation
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Research Associate |
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- Developing methods for large-scale protein structure modeling
- Structural characterization of macromolecular complexes
- Ligand-docking
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Mark Peterson |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- comparing sequence-structure relationships in orthologs vs. paralogs
- developing new methods for improving weighting of multiple templates for comparative modeling
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Jeremy Phillips |
Graduate Student |
Graduate Program in Biological and Medical Informatics |
- Restrained protein-protein docking in the context of large macromolecular assemblies
- Work toward a higher resolution of the structure of the Nuclear Pore Complex (NPC) by integration of diverse experimental data and computational modeling.
- Docking applications of the integrated modeling platform (IMP)
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Associate Researcher |
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- ModBase: A database of comparative protein structure models
- Target Selection and Annotation for Structural Genomics
- Comparative models for Molecular Replacement
- Systems Administration
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Postdoctoral Scholar |
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- integrative modeling of the dynamics of transport through the NPC
- optimizing the representational level of detail when modeling assemblies
- kinetic data structures and other means of maintaining geometric data structures on moving primitives
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Lab Head |
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Avner Schlessinger |
Postdoctoral Scholar |
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Javier Velazquez-Muriel |
Postdoctoral Scholar |
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- Ab-initio predicition of proteins with additional experimental data. Example, EM-maps.
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Research Associate |
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- Development of the Modeller package for comparative modeling.
- Development of the IMP platform for assemblies and modeling.
- Refinement of protein structure models.
- Systems administration.
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