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Computer-Aided Drug and Therapy Discovery Lab

Pan-omics

The most fundamental goal in drug design is to predict whether a given molecule will bind to a target and if so how strongly. Molecular mechanics or molecular dynamics are most often used to predict the conformation of the small molecule and to model conformational changes in the biological target that may occur when the small molecule binds to it. Semi-empirical, ab initio quantum chemistry methods, or density functional theory are often used to provide optimized parameters for the molecular mechanics calculations and also provide an estimate of the electronic properties (electrostatic potential, polarizability, etc.) of the drug candidate that will influence binding affinity.

Molecular mechanics methods may also be used to provide semi-quantitative prediction of the binding affinity. Also, knowledge-based scoring function may be used to provide binding affinity estimates. These methods use linear regression, machine learning, neural nets or other statistical techniques to derive predictive binding affinity equations by fitting experimental affinities to computationally derived interaction energies between the small molecule and the target.

Ideally, the computational method will be able to predict affinity before a compound is synthesized and hence in theory only one compound needs to be synthesized, saving enormous time and cost. The reality is that present computational methods are imperfect and provide, at best, only qualitatively accurate estimates of affinity. In practice it still takes several iterations of design, synthesis, and testing before an optimal drug is discovered. Computational methods have accelerated discovery by reducing the number of iterations required and have often provided novel structures.

Drug design with the help of computers may be used at any of the following stages of drug discovery:

  • hit identification using virtual screening (structure- or ligand-based design)
  • hit-to-lead optimization of affinity and selectivity (structure-based design, QSAR, etc.)
  • lead optimization optimization of other pharmaceutical properties while maintaining affinity

Dell Precision Tower 5810 Workstation

Intel® Xeon® processors: Power through the most demanding, interactive applications quickly with a new generation of single-socket performance with the Intel® Xeon® processor E5-1600 v3 series. The Dell Precision Tower 5810 delivers up to 75 percent better performance than previous generations for iterative design and prototyping.

Powerful graphics and memory: The latest NVIDIA® Quadro® and AMD FirePro™ graphics deliver the muscle you need to run the most demanding software applications. New Quadro and FirePro graphics offer larger dedicated graphics memory for your large data sets. System memory is expandable up to 256GB using the latest DDR4 RDIMM memory technology. The Dell Precision Tower 5810 delivers up to 5.5x higher graphics performance than previous generations on SolidWorks, 3.7x on CATIA, 5.5x on CREO, 6.8x on MAYA and 3.6x on Siemens NX.

High-performance storage: Choose the Dell actively cooled PCIe SSD storage solution for the fastest and most reliable way to store your content, up to 180% faster than traditional SATA SSD storage. If you prefer traditional storage options, choose the optional 12 Gb/s RAID controllers, doubling the I/O speed of our previous-generation Workstation.

The Milky Way II Supercomputer System

  • The Milky Way II supercomputer system, developed by the National University of Defense Technology (NUDT), is the outstanding achievement of the National 863 Program.
  • With 16,000 computer nodes, each comprising two Intel Ivy Bridge Xeon processors and three Xeon Phi coprocessor chips, it represents the world's largest installation of Ivy Bridge and Xeon Phi chips, counting a total of 3,120,000 cores. Each of the 16,000 nodes possess 88 gigabytes of memory (64 used by the Ivy Bridge processors, and 8 gigabytes for each of the Xeon Phi processors). The total CPU plus coprocessor memory is 1,375 TiB (approximately 1.34 PiB).
  • During the testing phase, the Milky Way II supercomputer system was laid out in a non-optimal confined space. When assembled at its final location, the system will have a theoretical peak performance of 54.9 petaflops. At peak power consumption, the system itself would draw 17.6 megawatts of power. Including external cooling, the system would draw an aggregate of 24 megawatts. The computer complex would occupy 720 square meters of space.
  • The front-end system consists of 4096 Galaxy FT-1500 CPUs, a SPARC derivative designed and built by NUDT. Each FT-1500 has 16 cores and a 1.8 GHz clock frequency. The chip has a performance of 144 gigaflops and runs on 65 watts. The interconnect, called the TH Express-2, designed by NUDT, utilizes a fat tree topology with 13 switches each of 576 ports.
MOE: an interactive, windows-based chemical computing and molecular modeling tool with a broad base of scientific applications.
Discovery studio: a software suite of life science molecular design solutions for computational chemists and computational biologists.
Pipeline Pilot: an environments to design, test, and deploy data processing procedures.
Amber:: a set of molecular mechanical force fields for the simulation of biomolecules; and apackage of molecular simulation programs which includes source code and demos.
AutoDock: AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.