GaudiMM: A modular multi-objective platform for molecular modeling. Rodríguez-Guerra Pedregal J, Sciortino G et al. J Comput Chem. 2017 Sep 15;38(24):2118-2126.
Structures of Medicago truncatula L-histidinol dehydrogenase show rearrangements required for NAD+ binding and the cofactor positioned to accept a hydride. Ruszkowski M, Dauter Z. Sci Rep. 2017 Sep 5;7(1):10476.
Differential replication of foot-and-mouth disease viruses in mice determine lethality. Cacciabue M, García-Núñez MS et al. Virology. 2017 Sep;509:195-204.
Katanin spiral and ring structures shed light on power stroke for microtubule severing. Zehr E, Szyk A et al. Nat Struct Mol Biol. 2017 Sep;24(9):717-725.
ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference. Dann GP, Liszczak GP et al. Nature. 2017 Aug 31;548(7669):607-611.(Previously featured citations...)
Chimera SearchGoogle Search
September 12, 2017
March 13, 2017
For a nice 3D-printing protocol that uses Chimera, see 3D Printing of Biomolecular Models for Research and Pedagogy by Da Veiga Beltrame, Tyrwhitt-Drake, et al. today in JoVE!
December 2, 2016(Previous news...)
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, nonprofit, and personal use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI), funded by the National Institutes of Health (NIGMS P41-GM103311).
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the RBVI, following UCSF Chimera.
Structures and their pocket measurements can be fetched directly from the Computed Atlas of Surface Topography of proteins (CASTp) database or read from local files previously returned by the CASTp server. In Chimera, the pockets are shown in a pocket list. Choosing rows in the list performs actions such as zooming in on pockets and selecting the surrounding atoms.
The figure shows the four largest pockets by volume identified by CASTp for PDB entry 1ovh (a cavity mutant of T4 lysozyme), shown in yellow, orange, pink, and magenta in order of decreasing volume. The largest is lysozyme's active site, with two openings. The second largest is the engineered cavity. Mutated positions are shown in red. Green balls are Cl– ions.(More features...)
Side-by-side views of a potassium channel structure (Protein Data Bank entry 1bl8) showing different approaches to cavity detection. On the left are molecular surface patches corresponding to the structure's two largest pockets by MS volume in the Computed Atlas of Surface Topography of proteins (CASTp) database. On the right is a tunnel in blue identified by the MolAxis server. Simple editing converted MolAxis output into a BILD file for display in Chimera. (More samples...)