Our laboratory is equipped with a variety of computational and experimental resources for the quantitative study of protein-ligand association.


Compute cluster

Compute (30 nodes)
2x Intel Xeon E5-2665 2.4GHz
256 GB memory
4x NVIDIA GPUs/node
GTX-680 [20 nodes]
GTX-Titan [10 nodes]
10GE ethernet
Exxact Corp 2U chassis/cooling

960 hyperthreaded cores - each node provides 32 hyperthreads with 8 GB/hyperthread

Torque/Moab batch queue scheduler and resource manager - provides advanced scheduling and reservation of CPU, GPU, memory, and license resources


Laboratory automation system overview

Thermo Fisher Momentum software - facilitates scheduling of multiple experiments simultaneously

Thermo BenchTrak Orbitorautomated 360-degree plate manipulator with internal regrip station, mounted on a 3.6m linear track. Used to integrate various other pieces of wet lab equipment into a single automation system.

Bionex HiG4 robotic centrifuge - microplate centrifugation up to 5000g

4x Inheco Incubator-Shaker DWP - bacterial culture and incubation in 96-well deepwell plates

Agilent PlateLoc - automated plate sealer

Agilent VCode - automated barcode printing and application for microplates

Thermo Cytomat Hotelfor random access to hundreds of microplates

Thermo MultiDrop Combi reagent dispenser - for rapid filling of microplates with common reagents

 

Tecan EVO 200automated liquid handling workstation equipped with air and liquid liquid-handling arms, robotic manipulator arm, vacuum manifold, heating/shaking stations, and Peltei

Tecan HP D300 - direct digital titration of compounds in DMSO

Tecan Infinite M1000PRO multifunction plate reader - equipped for absorption, fluorescence, fluorescence polarization, luminescence, and alphascreen assays, with injectors for kinetic assays

Caliper LabChip GX II - microfluidic quantitation and size analysis of proteins and nucleic acids

Roche LightCycler 480 - qPCR for standard PCR and thermofluor protein denaturation melts

Stratasys uPrint SE PLUS - 3D printer of ABSplus plastic for custom fabrication of SBS-format labware holders, with resolution down to .254mm

ServersCheck temperature/humidity probes. [current data feed]


Tecan EVO 200 liquid-handling workstation

Liquid Handling Arm (LiHa) - liquid-based syringe-actuated pipetting arm for dispensing volumes up to 1000 uL without the need for disposable pipette tips

Air LiHa - air based pipetting arm with disposable tips for accurate dispensing of 1-200 uL volumes

Tecan Te-VacS - vacuum station with two independently controlled vacuum manifolds

4x Torrey Pines EchoTherm RIC20 Peltier units - for heating and cooling

Robotic Manipulator Arm (RoMa) - robotic manipulator arm for manipulating labware on the deck

2x Inheco Thermoshake heating cooling shakersfor heating, cooling, and shaking while pipetting


Compound stock solution preparation

LabMinds Revo automated buffer maker - fully automated, reproducible, traceable preparation of buffers in liter quantities, requested by built-in tablet or on-the-go from your mobile device

Mettler-Toledo Quantos automatic gravimetric solution preparation system - powder and liquid dosing heads enable accurate preparation of compound solution stocks.

Integrated Mettler-Toledo QD206DR balance has 0.005mg @ 81g / 0.01mg @ 220g readability.


Density measurement

Mettler-Toledo DM40 density meter with 0.0001 g/cm3 accuracy, 0-3 g/cm3 range, and temperature measurement range of 0-91 C using 1 mL sample volumes.

Mettler-Toledo SC30 automated sample changer with 30-sample capacity

LabX ELN software for data management


Core facilities

Rockefeller HTSRC - The Rockefeller HTSRC provides a GE/MicroCal Auto iTC-200 automated low-volume microcalorimeter and a BioRad ProteOn XPR36 SPR system with 6x6 chip for parallel measurements of binding affinity and kinetics.

 

MSKCC analytical NMR facility - with a 600 MHz NMR and 40-sample changer for automating NMR measurements on protein and small-molecule samples


Banner image by Christina Johnson