Biomolecules in the computer: Jmol to the rescue

  title={Biomolecules in the computer: Jmol to the rescue},
  author={Angel Herr{\'a}ez},
  journal={Biochemistry and Molecular Biology Education},
  • A. Herráez
  • Published 1 July 2006
  • Chemistry
  • Biochemistry and Molecular Biology Education
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… 
Tools and Procedures for Visualization of Proteins and Other Biomolecules
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
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
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
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
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
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
  • Wei Zhang
  • Biology
    Methods 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
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.


An Introduction to Molecular Visualization: Seeing in Stereo with RasMol
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
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.
Recent changes to RasMol, recombining the variants.
RASMOL: biomolecular graphics for all.
Software review: BioROM 2005
  • Elba S Vazquez
  • Biology
    Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
  • 2004
The OpenScience Project, available on-line at
    available on-line at (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
      Java applets for displaying 3D mole- cule structures: An overview, available on-line at
      • 2004