Liang Lab Resources

Basic Molecular Biology and Plasmid Cloning 

Aseptic Techniques: Cell Culture Basics 

Key Steps of Molecular Cloning 

Affinity purification (His-tagged Proteins) 

PDB 101 

Crystallography 101 

Fourier Transform, Fourier Series, and frequency spectrum 

A brief overview of single-particle cryo-EM 

The 2017 Nobel Prize in Chemistry: Cryo-electron microscopy 

Image Preparation: Preparing your figures for publications - EM University  

CryoEM101  

Eva Nogales (UC Berkeley): Introduction to Electron Microscopy (47 min) 

Life Sciences Electron Microscopy Learning Center (Thermofisher)  

Drug Discovery Using Electron Microscopy (Thermofisher)  

Cryo-EM Atomic Resolution Webinar (Thermofisher)  

CZI for Advanced Biological Imaging workshop  

The Atlas of Bacterial & Archaeal Cell Structure (digital textbook)  

EM learning materials (Franklab at Columbia) 

S²C² Training: Annual Workshops & Lectures  

S2C2 workshops (Archived presentations)  

NRAMM Workshops  

NCCAT Courses  

Cold Spring Harbor Laboratory (CSHL)  

Laboratory for BioMolecular Structure (LBMS) at Brookhaven National Laboratory (BNL)  

Collaborative Computational Project No. 4 (CCP4) Workshop  

MRC EM Course  

LMB Cryo-EM course (2017)  

EMBO courses (2017)  

Birkbeck EMBO course (2019)  

Computational Methods for CryoEM 

EMAN2: Wiki and documentations of EMAN2 

EMAN2.1 - One hour to subnanometer resolution 

RELION 3.0 

DNASTAR Lasergene: Molecular Biology, Protein, and Genomics. For molecular cloning, create protein constructs 

EndNote: format bibliographies, find full text, and search for references 

NoMachine: Securely deliver Mac, Windows, Linux, web-based desktops and applications to any device 

MobaXterm: Enhanced terminal for Windows with X11 server, tabbed SSH client, network tools 

COOT [Crystallographic Object-Oriented Toolkit]: Macromolecular model building, model completion and validation 

CCP4 [Collaborative Computational Project Number 4]: Software for Macromolecular X-Ray Crystallography 

RELION [REgularised LIkelihood OptimisatioN]: Refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM) 

cisTEM [computational imaging system for transmission electron microscopy]: Process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions 

CryoSPARC [Cryo-EM Single Particle Ab-Initio Reconstruction and Classification]: Scientific software platform for cryo-electron microscopy (cryo-EM) 

PHENIX [Python-based Hierarchical ENvironment for Integrated Xtallography]: A comprehensive software package for macromolecular structure determination using crystallographic (X-ray, neutron and electron) and electron cryo-microscopy data 

PyMOL: (Request education copy) Molecular Visualization System  

UCSF Chimera / UCSF ChimeraX: Resource for Biocomputing, Visualization, and Informatics 

Inkscape: Equivalent to Adobe Illustrator 

Gimp: Equivalent to Adobe Photoshop 

SBGrid Consortium: The Liang Lab is a Member Lab of the Consortium. All the lab members has the access to the applications (> 450) listed at SBGrid Consortium. 

Cryo-Electron Microscopy (Cryo-EM):

National Center for CryoEM Access and Training NCCAT

Cryo-EM/ETStanford-SLAC Cryo-Electron Microscopy Facilities S2C2 

Pacific Northwest Center for Cryo-EM PNCC 

National Cancer Institute NCI

Brookhaven National Library BNL

CryoEM Purdue MW

The Southeastern Center for Microscopy of MacroMolecular Machines SECM2

Cryo-Electron Tomography (Cryo-ET):

CEMRC: The UW-Madison Cryo-Electron Microscopy Research Center (CEMRC)  

CU BOULDER CENTER FOR CRYO-ET

National Center for In-situ Tomographic Ultramicroscopy (NCITU) 

Stanford-SLAC CryoET Specimen Preparation Center 

X-Ray Crystallography:

APS SER-CAT Beamline Schedules (Chicago) 

BNL: (Stony Brook, NY)

S2C2: (Stanford, CA)

IEMC [Robert P. Apkarian Integrated Electron Microscopy Core]: negative stain electron microscopy (nsEM), single-particle cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), and scanning electron microscopy (SEM). Pay with PPMS. 

EIPC [Emory Integrated Proteomics Core]: Protein identification (in-gel or in-solution digestion), Interactome analysis (on-bead digestion), Post-translational modifications (PTM), Isobaric (TMT) and Label-free quantification, and Bioinformatic analysis support 

EIGC [Emory Integrated Genomics Core]: CLIA, Epigenetics, Genome Engineering, Genomics, and Passthrough 

Wyatt Technology DynaPro Plate Reader III: High-throughput, automated, dynamic and static light scattering 

NanoTemper Dianthus NT23.Pico: Take on challenging targets with plate-based affinity screenings 

BD FACSMelody™ Cell Sorter: approachable, affordable and automated 4-way cell sorting solution