DAPLDS A DYNAMICALLY ADAPTIVE PROTEINLIGAND DOCKING SYSTEM BASED ON

DAPLDS A DYNAMICALLY ADAPTIVE PROTEINLIGAND DOCKING SYSTEM BASED ON






DAPLDS: a Dynamically Adaptive Protein-Ligand Docking System based on Multi-Scale Modeling

DAPLDS: a Dynamically Adaptive Protein-Ligand Docking System based on Multi-Scale Modeling

 

Michela Taufer, Patricia J. Teller, Andre Kerstens, Trilce Estrada, David Flores, Guillermo Lopez, Richard Zamudio (University of Texas at El Paso)

David P. Anderson (University of California at Berkeley)

Roger Armen and Charles L. Brooks III (The Scripps Research Institute)

 

The DAPLDS project, or Dynamically Adaptive Protein-Ligand Docking System project, aims to build a computational environment to assist scientists in understanding the atomic details of protein-ligand interactions. High-throughput, protein-ligand docking simulations are performed on a computational environment that deploys a large number of volunteer computers (donated compute cycles) connected to the Internet.

 The scales proposed in DAPLDS are not the traditional scales currently used in the life sciences. We deal with computational rather than experimental multi-scales. Our multi-scale approach comprises three spanning scales (dimensions) of docking assumptions: protein-ligand representation, solvent representation, and sampling strategy. Within a scale, different scale values require different models and different algorithms to represent the models.

 In such a scenario, the two most critical challenges in dealing with multiple scales computationally are: (1) the ability to model biological systems with algorithms that dynamically adapt to the most appropriate value of each scale and (2) the ability to assure that the algorithms can, indeed, be executed in the “required” amount of time using large numbers of distributed volunteer computing systems. The latter point refers to having the necessary computational resources (CPU cycles, memory, network, etc.). The nature of these challenges requires collaboration among computational biophysicists, computational scientists, computer scientists, and system architects. These challenges and our main achievements are presented in this poster.

 

 






Tags: adaptive protein-ligand, dynamically adaptive, system, daplds, docking, dynamically, adaptive, proteinligand, based