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Example of HIV-1 protease binding site flexibility

DAPLDS: A Dynamically Adaptive Protein-Ligand Docking System Based on Multi-Scale Modeling 

Contents

• Contact Information
• Funding Agency 
• Research Emphasis 
• Scales Examined 
• Biomedical, Biological &  Behavioral Areas
• Modeling Methods & Tools  
• Software Development 

Contact Information

Principal Investigator/Contact
Michela Taufer
University of Texas at El Paso
Phone: (915) 747-6957
Fax: (915) 747-5030
E-mail: taufer@acm.org
Project web site: http://research.utep.edu/daplds

Co-PIs and Collaborators
Patricia J. Teller
Computer Science Department
University of Texas at El Paso 
Area of expertise: Modeling for dynamic adaptation

Martine Ceberio
Computer Science Department
University of Texas at El Paso
Area of expertise: Decision theory

Charles L. Books III
Computational Biophysics and Chemistry
The Scripps Research Institute (TSRI)
Area of expertise: Docking methods

David P. Anderson
Science Space Laboratory
University of California, Berkeley
Area of expertise: Volunteer computing 

Grant Number - 506429

Funding Agency

National Science Foundation (NSF)

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Research Emphasis

DAPLDS (Dynamically Adaptive Protein-Ligand Docking System) is a cybertool that enables adaptive multi-scale modeling in a global computing environment (i.e., distributed, heterogeneous computing environment using "volunteer" PC computers). This project will further knowledge of the atomic details of protein-ligand interactions. By doing so, it will accelerate the discovery of novel pharmaceuticals.

The goals of the project are: (1) to explore the multi-scale nature of algorithmic adaptations in protein-ligand docking and (2) to develop cyber infrastructures based on computational methods and models that efficiently accommodate these adaptations.

The intellectual merit of the project derives from small molecules called ligands. Ligands play an essential role in turning protein functions on or off, or in providing substrates for chemical reactions catalyzed by enzymes. Knowledge of the atomic level details of the protein-ligand docking is a valuable resource in the development of novel pharmaceuticals.

This project changes the way in which grand challenges are approached by implementing an adaptive cybertool that scales beyond the protein-ligand docking application. For example, this tool can be adapted and used for protein folding and protein structure prediction. Moreover, the use of public computing resources promotes and disseminates science research and science knowledge among the users of PCs involved in this effort. 

Abstract

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Scales Examined 

Time Scales

• Nanosecond and below (ns)
• Microsecond (μs)

Biological Scales

• Atomic
• Molecular
• Molecular Complexes

Length Scales 

• Nanometer and below (nm)

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Biomedical, Biological and Behavioral (BBB) Areas and Percent Focus

35% - Characterize mobility behavior of branched polypeptides during electrophoresis at various levels of entanglement with an immobile matrix

Modeling Methods and Tools (MMT)Areas and Percent Focus

65% - Monte Carlo (MC), Molecular Dynamics (MD) simulations

Software Development