Chiu Laboratory
Cryo-EM of Membrane Proteins
May 07, 2022.
Chiu Laboratory
Cryo-EM of Membrane Proteins
May 07, 2022.
3D Complex
3D Complex is a hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins.
3D-FSC
The 3D-FSC provides a quantitative measure of directional resolution anisotropy, which is caused by preferential orientation at the air-water interface, as described in Tan et al 2017.
AlphaCryo4D
AlphaCryo4D is an open-source free software that implements 3D classification of single-particle cryo-EM data using deep manifold learning and novel energy-based particle voting methods.
Bsoft
Bsoft is a collection of programs and a platform for development of software for image processing in structural biology.
CAVER
CAVER is a software tool for analysis and visualization of tunnels and channels in protein structures.
CCP-EM
The Collaborative Computational Project for electron cryo-microscopy (CCP-EM) supports users and developers in biological EM.
CNS
Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
Computational Crystallography Toolbox (cctbx)
The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the PHENIX system.
cryo-EF
An open-source software package for robust analysis of the orientation distribution of cryoelectron microscopy data.
ctffind, ctftilt
CTFFIND3 and CTFTILT are two programs for finding CTFs of electron micrographs.
EMAN2
EMAN2 is a scientific image processing suite with a primary focus on processing TEM image data. It provides various tools useful in structure determination for cryo-EM.
EMDA
EMDA is a Python library for Electron Microscopy map and model manipulations. It comes under MPL-2.0 license. It supports both Python3 and Python2.
Focus
The interface between data collection and data processing in cryo-EM.
Gautomatch & Gctf
The programs of automated particle picking and CTF estimation that utilizes the GPU resources.
LigPlot+
LigPlot+ is a successor to our original LIGPLOT program for automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface which allows on-screen editing of the plots via mouse click-and-drag operations.
LocScale
LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods.
MotionCor2
The multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with automated data collection. The result is an exceptionally robust strategy that can work on a wide range of data sets, including those very close to focus or with very short integration times, obviating the need for particle polishing.
Oxford Particle Imaging Centre
Repository for Scipion, the scripts for local reconstruction, wrapped Python scripts for Relion, and so forth.
Pro-Origami
Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.
ProSHADE
ProSHADE (Proitein SHApe DEscription and symmetry detection) is a library and an associated tool providing functionalities for working with structural biology molecular structures. The library implements functions for computing shape-wise structural distances between pairs of molecules, detecting symmetry over the centre of mass of a single structure, map re-sizing as well as matching density maps and PDB coordinate files into one another.
PyMOL
PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
SerialEM
SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods.
SPIDER & WEB
SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.
UCSF Chimera
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.
2DX
2dx is an initiative that aims at facilitating computer image processing in electron crystallography.
IPLT
The Image Processing Library & Toolbox is an open-source project, released under the GNU General Public License. It is primarily aimed at the electron microscopy community, with particular emphasis on 2D electron crystallography.
APBS & PDB2PQR
APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems.
CCP4
CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.
CMCD in Gromacs
The correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map.
cryoID
cryoID is a python-based program that determines the unique identity of the protein(s) in unknown near-atomic resolution cryoEM density maps from a pool of candidate protein sequences.
DeepTracer
The fully automatic tool for de novo all-atom protein complex structure prediction from cryo-electron microscopy (cryo-EM) density maps using 3D deep learning. (Pfab et al. (2020))
EMBuilder
EMBuilder is a model building program for cryo-EM density maps. It is based on template matching method which is widely used in Crystallography. The suitable resolution for input map is higher than 3.5 Å.
EMRinger
This is the set of scripts used for the EMRinger paper (citation below). For the most up-to-date version of EMRinger, please use phenix.emringer or the integrated GUI version of EMRinger in the latest phenix nightly.
Fitmunk
Fitmunk provides a framework for fitting conformations on a fixed backbone into electron density.
ISOLDE
ISOLDE is a modern, immersive environment designed to ease the historically challenging task of building high-quality macromolecular models into low to medium resolution experimental maps.
Modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.
OpenMM
OpenMM includes everything one needs to run modern molecular simulations. It is extremely flexible with its custom functions, is open-source, and has high performance, especially on recent GPUs.
OpenStructure
Open-Source Computational Structural Biology Framework.
Phenix
PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Rosetta
Rosetta is a comprehensive software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. (Rosetta Commons; https://www.rosettacommons.org)
RoseTTAFold
Accurate prediction of protein structures and interactions using a 3-track network.
SCWRL4
SCWRL4 predicts the side-chain conformations. (G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009).)
TomoSegMemTV
TomoSegMemTV is a software package for segmenting membranes in tomograms. It is based on (1) a Gaussian-like model of membrane profile, (2) a local differential structure approach and (3) anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures.The method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The software TomoSegMemTV is provided as a set of Matlab functions. The kernels of the most computation-intensive operations were coded in C++ using code optimization and multithreading and are provided as binaries to be used within Matlab.
cisTEM
cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It was developed by Tim Grant, Alexis Rohou and Nikolaus Grigorieff and comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
cryoSPARC
CryoSPARC™ is an easy to use software tool that enables rapid, unbiased structure discovery of proteins and molecular complexes from cryo-EM data.
Frealign
Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles.
Relion
RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in cryo-EM.
Scipion
Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers.
THUNDER
A particle-filter framework for robust cryoEM 3D reconstruction.
Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Martini
The Martini force field is a coarse-grain (CG) force field suited for molecular dynamics simulations of biomolecular systems. The force field has been parametrized in a systematic way, combining top-down and bottum-up strategies: Non-bonded interactions are based on the reproduction of experimental partitioning free energies between polar and apolar phases of a large number of chemical compounds, whereas bonded interactions are derived from reference all-atom simulations.
MDAnalysis
MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools. -
Scripts for Topaz use in Relion
These scripts allow you to run TOPAZ particle picker and denoiser (https://github.com/tbepler/topaz) from the RELION (https://github.com/3dem/relion) gui as an External job type.
UCSF PyEM
UCSF pyem is a collection of Python modules and command-line utilities for electron microscopy of biological samples.
CTF calculator
This page is written by Takanori Nakane at MRC-LMB. This page uses Javascript for calculation.
Cython
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
DASK
Dask provides advanced parallelism for analytics, including Scikit, RAPDIS, MDAnalysis, and so on.
matplotlib
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.
The Hitchhiker’s Guide to Python
This opinionated guide exists to provide both novice and expert Python developers a best practice handbook to the installation, configuration, and usage of Python on a daily basis.
PyCUDA
PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.
PyQtGraph
PyQtGraph is a pure-python graphics and GUI library built on PyQt4, PySide and numpy. It is intended for use in mathematics, scientific, engineering applications. Despite being written entirely in python, the library is very fast due to its heavy leverage of numpy for number crunching and Qt’s GraphicsView framework for fast display.
Higra
Higra is a C++/Python library for efficient sparse graph analysis with a special focus on hierarchical methods.
High-performance computing
Hardware
Resource
Utiilities in modeling
Scientific programming