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Department of Biostatistics & Bioinformatics,Duke University

“USING HIGH-THROUGHPUT DATA TO DERIVE NEW MODELS OF PROTEIN-DNA BINDING SPECIFICITY”

Raluca Gordân​Transcription factors (TFs) regulate gene expression by binding to specific, short DNA sites in the promoters or enhancers of the genes they regulate. Most eukaryotic TFs are members of large protein families that share a common DNA binding domain and thus have similar binding specificities. However, paralogous TFs (i.e., members of the same family) typically perform different regulatory functions in vivo by binding to different sets of genomic sites. Current models for DNA binding specificity, such as position weight matrices (PWMs), cannot typically distinguish among the DNA sites bound by paralogous TFs. This significantly restricts our ability to computationally predict genomic targets for individual members of TF families. I will describe new regression-based models for TF-DNA binding specificity, that are able to capture differences among closely-related TFs even when their PWMs are virtually identical. We train our models using high-throughput in vitro data from custom protein binding microarray (PBM) experiments. Our PBMs are specifically designed to cover a large number of potential TF-DNA binding...

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Department of Chemistry, University of South Florida

“LIGHTING-UP METAL ORGANIC FRAMEWORKS: PHOTOCATALYTIC GUEST ENCAPSULATION IN METAL ORGANIC FRAMEWORKS”

Metal organic frameworks (MOFs) have emerged as an important class of porous materials noted for extremely high surface areas, functionalizable building blocks, and ease of synthesis. To date, a plethora of MOFs have now been synthesized and their physical properties examined with a focus on gas storage and separation. The catalytic diversity of MOFs, on the other hand, is emerging as an important area of MOF functionality with photo-catalysis a primary target of investigation. Two general strategies have been employed in the development of MOFs as photo-catalysts. The first utilizes the metal cluster building blocks and/or the ligands composing the framework as the photo-active component of the MOF. These photo-active framework MOFs typically contain lanthanide metal clusters or porphyrin based organic linkers which are both photo-chemically active. Alternatively, recent advances have been made in the development of MOFs in which the ligands connecting the metal clusters are composed of either free base or metallo-porphyrins. The advantages of this type of MOF photo-catalyst include a high density of available catalytic sites, ease of access of photochemical reactants and the ability to tune the framework to be selective...

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Department of Physics and Astronomy,Kinard Laboratory Building,Clemson University

“IMPROVING THE PHYSICS AND SPEED OF DELPHI POISSON-BOLTZMANN SOLVER”

​Emil AlexovElectrostatic forces and energies are one of the major components of the total energy of biological macromolecules. However, computing the electrostatic field distribution in systems made of biological objects immersed in water is not trivial task because of the large degree of freedom associated with the water phase, which in general limits the applications of explicit model to system with sizes smaller than several hundred Angstroms. This problem is avoided by applying continuum electrostatic approaches to deliver the potential distribution, considering that the water and macromolecules are two distinctive dielectric media. Here we report development and implementation in DelPhi of a Gaussian model for atomic densities and its usage to deliver a smooth dielectric function. The performance of the Gaussian DelPhi was benchmarked against solvation energies of small molecules obtained with explicit water simulations and very good agreement was found. The Gaussian DelPhi was also shown to perform much better than standard calculations in delivering the potential distribution is the...

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