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 Orbitor - automated 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 Hotel - for random access to hundreds of microplates

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

Opentrons OT-2 - small, customizable liquid handling robot controlled using open-source Python code. 

Tecan EVO 200 - automated 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

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 shakers - for heating, cooling, and shaking while pipetting

Compound stock solution preparation Compound storage

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

Roylan Developments Ltd StoragePods - multichannel compound storage unit to prevent moisture absorption of samples. Storage capacity of 252 shallow well plates or 72 tube racks. [controller] [storage units]

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.

Column chromatography

Four-tiered Bio-Rad NGC Quest 10 Plus Chromatography System - for column chromatography. Equipped with 10 mL/min pumps, multi-wavelength (UV/Vis) and conductivity detectors, pH sensing, automated sample injection, buffer blending valve, with the capacity to run multiple columns in succession.  

Fisherbrand Dispensing Peristaltic Pump to filter solutions before applying to chromatography systems.

Thermodynamic measurements

Malvern MicroCal Peaq-ITC Automated for automated thermodynamic measurements of biomolecular interactions with the capacity to run up to four 96-well plates per experiment.

 

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