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Meiler Lab Computational Chemical and Structural Biology |
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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 RosettaTMHApplications
Modeling of Protein IIIA Structure Determination of DsbB using Paramagnetic Restraints Structure determination of KCNE3 using paramagnetic restraints
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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 DataApplications
Modeling Rhodopsin Interaction with G-Protein and Arrestin Mechanism of Activation of the heterotrimeric G protein alpha subunit
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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 ModelingApplications
mGluR5 Related Neurological Diseases Allosteric Modulators of Neuropeptide Y Receptors Malaria - Inhibition of beta-Hematin Crystallization in Plasmodium falciparum Rapid in silico target identification for anti-malarials
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Methods Development
Rosetta Drug Design Rosetta Design Modeling Partial Covalent Interactions in Protein Ligand Interfaces RosettaLigandEnsemble Drug Design through Foldit Video GameApplications
Structural Determinants of Antidepressant Drugs GPCR Model Building, Refinement, and Ligand Docking HIV-1 Protease Inhibitor Docking Protein-Ligand Interaction as Cancer Therapeutics
Modeling of Protein IIIA
The BCL method for elucidating a protein fold using Cryo-EM data has been applied to human adenovirus protein IIIa. This protein, for which there is no high resolution structure, is predicted to be highly α-helical. It is resolved in a 6.8Å resolution cryoEM adenovirus structure as a bundle of 14 α-helical density rods. A partial model where 11 out of 14 α-helices are predicted with a high confidence has been built for this crucial adenovirus capsid protein.
Alumni Project Members: Steffen Lindert
Center for Structural Biology
465 21st Ave South, BIOSCI/MRBIII
Vanderbilt University, Nashville, TN