Biomolecules in the computer: Jmol to the rescue
@article{Herrez2006BiomoleculesIT, title={Biomolecules in the computer: Jmol to the rescue}, author={Angel Herr{\'a}ez}, journal={Biochemistry and Molecular Biology Education}, year={2006}, volume={34} }
Jmol is free, open source software for interactive molecular visualization. Since it is written in the Java™ programming language, it is compatible with all major operating systems and, in the applet form, with most modern web browsers. This article summarizes Jmol development and features that make it a valid and promising replacement for Rasmol and Chime in the development of educational materials, as well as in basic investigation of biomolecular structure. The description is set up by…
320 Citations
Tools and Procedures for Visualization of Proteins and Other Biomolecules
- BiologyCurrent protocols in molecular biology
- 2015
Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms. An enormous amount of structural data for a large number of these biomolecules has been…
Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability
- Computer Science
- 2008
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an…
Conscript: RasMol to PyMOL script converter
- Computer ScienceBiochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
- 2010
ConSCRIPT, the first SBEVSL release, is a plug‐in for PyMOL that accepts RasMol scripting commands either as premade scripts or as line‐by‐line entries from PyMol's own command line.
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol
- Computer ScienceBioinform.
- 2007
UNLABELLED
SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with…
IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes
- Biology, ChemistryBioinform.
- 2015
A web-based tool, Integrative Biology of Sequences and Structures (IBiSS), which is designed for interactively displaying 3D structures and selected sequences of subunits from large macromolecular complexes thus allowing simultaneous structure-sequence analysis such as conserved residues involved in catalysis or protein-protein interfaces.
AMIPRO: A Content-Based Search Engine for Fast and Efficient Retrieval of 3D Protein Structures
- Computer Science, Biology
- 2018
The proposed search engine model will result in an efficient and fast retrieval of similar protein structures by taking into account the visual/structure-based similarity and the information contained in the data sets rather than the traditional sequence-based searching.
Computer-Aided Drug Discovery
- BiologyMethods in Pharmacology and Toxicology
- 2016
The basics of molecular dynamics simulation are covered, in the hopes that a reader would be able to intelligently conduct a simulation of their favorite protein(s), analyze the results in order to make hypotheses about the links between protein dynamics and conformation.
SWIFT MODELLER v2.0: a platform-independent GUI for homology modeling
- Computer ScienceJournal of Molecular Modeling
- 2011
SWIFT MODELLER v2.0 provides an interactive homology modeling solution by automating the formatting, scripting, and data extraction processes, meaning that the user only needs to paste in the protein target sequence as input.
References
SHOWING 1-10 OF 27 REFERENCES
An Introduction to Molecular Visualization: Seeing in Stereo with RasMol
- Chemistry
- 1997
Just as protein and nucleic acid sequences are collected in databases accessible on the Internet, so too are three-dimensional structures from X-ray crystallography and nuclear magnetic resonance…
The Protein Data Bank
- ChemistryNucleic Acids Res.
- 2000
The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Software for reviewing biomolecules in three dimensions on the Internet.
- Computer Science, MedicineTrends in biochemical sciences
- 1995
Software review: BioROM 2005
- BiologyBiochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
- 2004
The OpenScience Project, available on-line at openscience.org
available on-line at www.biorom.uma.es (A collaborative project, with 25 authors from 15 Universities; also available on CD-ROM
- BioROM: Aids for learning Biochemistry, Biotechnology and Molecular Biology (in Spanish)
- 2004
OCA©, a browser database for protein structure/function, available on-line at bip.weizmann.ac.il/oca-docs/oca-home
Java applets for displaying 3D mole- cule structures: An overview, available on-line at www.dkfzheidelberg.de/spec/staff/bohne/javamol/index.html
- 2004