Tag: Java

J3DPSV 1.0 – Java Three-dimensional (3D) Protein Structure Viewer

J3DPSV 1.0

:: DESCRIPTION

J3dPSV is a graphical application package for viewing and modeling of three dimensional structures of protein structure, including multiple chain sequence table and a three-dimensional (3D) protein structure viewer.

:: DEVELOPER

Hyun Seok Park

:: SCREENSHOTS

J3DPSV

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 J3DPSV

:: MORE INFORMATION

Citation

Chun, Yoo Jin, Il Ham, Seong, Yang, San Duk, Rhie, Arang, Park, Hyun Seok
Refactoring the code for visualizing protein database information in a 3D viewer for software reusability
Genomics & Informatics, 6:50-53, MAR 31 2008

jPCR 1.15.8 – Java Tools for PCR, in silico PCR, Oligonucleotide Assembly & Analysis

jPCR 1.15.8

:: DESCRIPTION

jPCR is a java application based on FastPCR software and provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, unique, group-specific, bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR); and microarray design;

::DEVELOPER

PrimerDigital

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

jPCR

:: MORE INFORMATION

Citation

Kalendar R, Lee D, Schulman AH 2011.
Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.
Genomics, 97(7).

HyperTree 1.2.2 – Java Phylogenetic Tree Viewer

HyperTree 1.2.2

:: DESCRIPTION

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.

::DEVELOPER

kinase.com

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 HyperTree

:: MORE INFORMATION

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1

NeoBio 1.0 pre-alpha – Sequence alignment algorithms in Java

NeoBio 1.0 pre-alpha

:: DESCRIPTION

NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.

::DEVELOPER

Sérgio Anibal de Carvalho Junior

 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 NeoBio

:: MORE INFORMATION

NeoBio is free software, so feel free to download and use it at your own will.

MCDL 20070701 – Java Molecular Viewer/Editor for Chemical Structures

MCDL 20070701

:: DESCRIPTION

MCDL (Modular Chemical Descriptor Language) is a small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.  The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI).

::DEVELOPER

Sergei Trepalin (Institute of Physiologically Active Compounds RAS)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

MCDL

:: MORE INFORMATION

Citation:

Molecules 2006, 11(4), 219-231; doi:10.3390/11040219
A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL)
Sergei V. Trepalin, Alexander V. Yarkov , Igor V. Pletnev and Andrei A. Gakh

JyMOL 1.0 – Java-based Molecular Visualization

JyMOL 1.0

:: DESCRIPTION

JyMOL, a Java-based development component, enables developers to easily create molecular visualization programs, browser applets, and JavaWS applications, replacing the visualization expert otherwise needed to build a specialized visualization component. The JyMOL API was designed to obviate the learning curve for users familiar with the PyMOL API.

::DEVELOPER

Schrödinger, LLC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JyMOL

:: MORE INFORMATION

Citation

The JyMOL Molecular Graphics System, Schrödinger, LLC.

Chemis3D 2.89b – Java 3D Molecular Viewer Applet

Chemis3D 2.89b

:: DESCRIPTION

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.

Chemis3D is a small applet running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.

Features

  • Real-time manipulation and fast 3D rendering.
  • Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .
  • Enhanced interface using popumenu and key shortcuts .
  • Multi-models display and molecular animation capabilities.
  • Measuring and analysing tools.
  • Support of the most popular molecular data formats :Brookhaven Protein DataBank (*.pdb).MSC XMol files (*.xyz).MDL molfiles (*.mol).

::DEVELOPER

Didier COLLOMB

:: SCREENSHOTS

:: REQUIREMENTS

  • Java-enabled browser

:: DOWNLOAD

Chemis3D 2.89b

:: MORE INFORMATION

Chemis3D MAY BE FREELY USED FOR PERSONNAL, ACADEMIC AND NON-COMMERCIAL PURPOSES, IN AGREEMENT WITH THE FOLLOWING RESTRICTIONS.

Exit mobile version