Index for Research Pages

Protein de-novo Folding

• Methods Development
  • Contact Prediction
  • BCL Align Sequence Alignment and Fold Recognition
  • Sparse EPR Data Guided Protein Structure Elucidation
  • Jufo9D Secondary Structure and TM Span Prediction
  • Protein Structure Prediction Using Fold Templates
  • BCL::Cluster: Clustering Biological Molecules with PyMOL Visualization
  • Gradient Minimization for Structure Refinement
  • RosettaTMH
• Applications
  • Modeling of Protein IIIA
  • Structure Determination of DsbB Using Paramagnetic Restraints
  • Structure Determination of KCNE3 Using Paramagnetic Restraints

Protein Structure Prediction from Sparse Data

• Methods Development
  • Protein Structure Prediction
  • Cryo-EM Fit
  • Cryo-EM Guided Protein Fold Elucidation
  • Membrane Protein Structure Prediction Using Sparse NMR Restraints
  • RosettaEPR
  • BCL::EMFitMinimize
  • Protein STructure Prediction Using SAXS Data
• Applications
  • Modeling Rhodopsin Interaction with G-Protein and Arrestin
  • Mechanism of Activation of the Heterotrimeric G Protein Alpha Subunit

Cheminformatics

• Methods Development
  • Chemical Shift Prediction
  • PharmMap
  • Method Development for QSAR Ligand-Based Virtual Screening
  • Development of RosettaQSAR
  • Knowledge-Based Small Molecule Conformational Sampling
  • Novel HTS Datasets Composed to Benchmark Ligand-Based QSAR Modeling
• Applications
  • mGluR5 Related Neurological Diseases
  • Allosteric Modulators of Neuropeptide Y Receptors
  • Malaria – Inhibition of beta-Hematin Crystallization in Plasmodium falciparum
  • Rapid in silico target identifiication for anti-malarials

Protein-Protein Interactions

• Applications
  • Structural Characterization of HoxA11
  • HIV Antibody/Antigens Interactions
  • Antibiotics – Protein/Peptide Interfaces
  • Antibody/Antigens Interaction

Ligand Docking

• Methods Development
  • Rosetta Drug Design
  • Rosetta Design
  • Modeling Partial Covalent Interactions in Protein Ligand Interfaces
  • RosettaLigandEnsemble
  • Drug Design Through Foldit Video Game
• Applications
  • Structural Determinants of Antidepressant Drugs
  • GPCR Model Building, Refinement, and Ligand Docking
  • HIV-1 Protease Inhibitor Docking
  • Protein-Ligand Interaction as Cancer Therapeutics

Protein Design

• Applications
  • Evolution of TIM Barrels
  • Chemical Basis of Ligand-Macromolecule Recognition