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http://www2.mrc-lmb.cam.ac.uk/
The MRC Laboratory of Molecular Biology (LMB) has long been, and remains, a world-class research laboratory. Our primary goal is to understand biological processes at the molecular level, through the application of methods drawn from physics, chemistry and genetics. This quest extends from structural studies of individual macromolecules, through their interactions and beyond to the functioning of subcellular systems, cells and multicellular systems in whole organisms, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. The LMB is one of the birthplaces of modern molecular biology. Many techniques were pioneered at the laboratory, most notably methods for determining the three-dimensional structure of proteins and DNA sequencing. Whole genome sequencing was initiated at the LMB. Another landmark discovery was the invention of monoclonal antibodies. Over the years, the work of LMB scientists has attracted 9 Nobel Prizes, shared between 13 LMB scientists, as well as numerous other prizes and scientific awards.
Proper citation: MRC Laboratory of Molecular Biology (RRID:SCR_003527) Copy
http://www.transcriptionfactor.org/index.cgi?Home
Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.
Proper citation: DBD: Transcription factor prediction database (RRID:SCR_002300) Copy
https://github.com/jefferis/nat
Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_017248) Copy
http://scop.mrc-lmb.cam.ac.uk/scop/
The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases.
Proper citation: SCOP: Structural Classification of Proteins (RRID:SCR_007039) Copy
http://www.ccp4.ac.uk/html/aimless.html
Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity.
Proper citation: AIMLESS (RRID:SCR_015747) Copy
A database of genomic and protein data for Drosophila site-specific transcription factors.
Proper citation: FlyTF.org (RRID:SCR_004123) Copy
http://grigoriefflab.janelia.org/ctffind4
Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.
Proper citation: CTFFIND (RRID:SCR_016732) Copy
http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/introduction.html
Software which processes diffraction data/images and produces an MTZ file of reflection indices with their intensities, standard deviations, and other parameters. The MTZ file is passed onto other programs of the CCP4 program suite for further data reduction. iMosflm processes data from CCD and pixel detectors. It is available for Windows, Mac OSX and Linux platforms. Tutorials are available at the website.
Proper citation: iMosflm (RRID:SCR_014217) Copy
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software for macromolecular model building, model completion and validation, and protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, rigid-body fitting, ligand search, Ramachandran plots, non-crystallographic symmetry and more. Source code is available.
Proper citation: Coot (RRID:SCR_014222) Copy
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