LinuxLinks.com
Newbies What Next ? News Forums Calendar
Home | Register | News | Forums | Portal Pages | MyLinks | New | Hot | Link Us

Search/Browse

 Category Gateway
More Options
Category:  


LinuxLinks News
 · Nifty Free Image Viewers
 · Compact Text Editors Great for Remote Editing and Much More
 · Excellent Subtitle Editors
 · Small Console Menu Utilities
 · Make Downloading Files Effortless
 · Free Office Suites that Cut The Mustard
 · Low-Spec Hardware? Try these Desktop Environments
 · Powerful Command-line File Transfer Programs
 · Great Apps to Take Notes
 · Exciting New Terminal Emulators
(more...)

 

Latest Links
jdkdrum
lolcat
(more...)

 



Top : Software : Scientific : Chemistry : Miscellaneous

Highlights
Nifty Free Image Viewers
One of my favorite adages is "A picture is worth a thousand words". It refers to the notion that a still image can convey a complex idea. Images can portray a lot of information quickly and more efficiently than text. They capture memories, and never let you forget something you want to remember, and refresh it in your memory.

(Read more)
Objectivity/DB
(commercial) A multi-threaded database engine with a rich set of development and administration tools.

Links:

  • ATK
    (commercial) ATK is a first principles electronic structure program capable of modelling electrical properties of nanostructured systems coupled to semi-infinite electrodes. The two electrodes, for instance, could be a nanotube and a metal, and the nanostructure could be the interface region between the two systems. Other typical systems include molecules between metal surfaces and interfaces between materials.
  • Chemical Structures
    The Chemical Structures project aims to provide a complete set of 3D molecular structures in CML format. As CML format permits structural data and many properties to be included, each file also contains additional information, like molecular weight, boiling point, melting point, or InChI code. Data can be explored with a CML-aware software, like Jmol, or by using a Web browser.
  • Chemical2vmd
    Chemical2vmd lets you use the Babel interface of VMD to load various molecular coordinate files via the .mailcap interface used by web clients like Mosaic or Netscape.
  • COPASI
    COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).
  • CRYSTAL
    (commercial) CRYSTAL computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations.
  • Dockres
    Dockres reads the log file of docking runs performed by Autodock and extracts the top scoring poses subject to various filters.
  • eHiTS
    eHiTS (Electronic High Throughput Screening) is a program for flexible docking of ligands to proteins. It is fast, fully automated, and comprehensively covers the searc space.
  • FlipDCD
    FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm, and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another.
  • Glide
    (commercial) Glide offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level.
  • Ionize
    Ionize is a threaded program for placing counterions near a biological molecule in preparation for molecular dynamics simulations.
  • MCTDH
    MCTDH stands for Multi Configuration Time Dependent Hartree. MCTDH is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces.
  • mctdhtools
    The mctdhtools project aims to provide a set of routines for easily reading and manipulating the output of the Heidelberg MCTDH code.
  • MDAPI
    The purpose of the MDAPI (molecular dynamics applications programming interface) is to provide a high performance C programming interface for the separation of code for molecular dynamics (MD) simulations into a front end and a computational engine.
  • MDEnergy
    MDEnergy is a program to calculate energies from DCD or PDB-files.
  • Molegro Virtual Docker
    (commercial) Molegro Virtual Docker is an integrated platform for predicting protein - ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.
  • MOPAC7
    MOPAC7 is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
  • MULTIMODE
    (commercial) MULTIMODE does Vibrational Self Consistent Field (VSCF) and several types of "CI" calculations for the rovibrational energies and wavefunctions of polyatomic molecules, transition states, clusters, etc.
  • Mychem
    Mychem is an extension that provides a set of functions that permit you to handle chemical data within a MySQL database.
  • OSET
    OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses.
  • POLYRATE
    POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species
  • Shop
    (commercial) Shop is a guide to .the Scaffold Hopping procedure during the Drug Discovery process. Scaffold Hopping is the methodology that substitutes one part of a molecule with another one, retaining their pharmacophoric interaction points.
  • Symmetry
    Symmetry is a set of C codes for automatic molecular symmetry recognition.
  • Triton
    Triton is graphical tool for modelling protein mutants and assessment of their activities. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER.
  • VAMP
    (commercial) VAMP is a semi-empirical molecular orbital package for molecular organic and inorganic systems. It is capable of calculating many physical and chemical molecular properties very rapidly. Its speed, stability, and reliability make it ideally suited to use for high-throughput screening in areas such as computational drug discovery.



Share this Page
Bookmark and Share
Submit this page to popular social networks such as Digg, Twitter, StumbleUpon and more.


My LinuxLinks
MyLinks
  • Bookmarked links
  • Emailed Newsletter
  • Your own profile

  • Top Applications
    Top Free Software
    6 Lean Desktops
    14 File Managers
    21 Backup Tools
    21 Window Managers
    21 Productivity Tools
    21 Text Editors
    21 Video Emulators
    21 Home Emulators
    42 Graphics Apps
    42 Scientific Apps
    42 Email Apps
    12 Instant Messaging
    42 Games
    42 More Games
    21 More Games
    42 Audio Apps
    42 Video Apps
    80 Security Apps
    Free Console Apps
    14 Multimedia
    'Free' Proprietary
    21 Closed-Source Apps
    Top Commercial Apps
    42 Games
    Free Web Software
    21 Web CMS
    14 Wiki Engines
    8 Blog Apps
    6 eCommerce Apps
    Other Articles
    Migrating from Windows
    Distribution Guide
    Distro Portal Pages

    Migrate to Linux
    Thinking of switching to Linux? Check out our Linux Equivalents to Windows Software section, highlighting popular Linux equivalents to Windows software.

    This feature also includes over 150 individual software portal pages including Blender, Scribus, OpenOffice.org, Evolution, Eclipse, K3b, and MythTV, providing a wealth of essential information.

     

    Distribution Guides
    Distro Guide

    Debian
    Fedora
    Gentoo
    Mandriva
    OpenSuSE
    RedHat
    Slackware
    Ubuntu
    Xandros

    Absolute
    Linux Mint
    64 Studio

    LiveCDs
    Berry Linux
    GoblinX
    KNOPPIX
    Kubuntu
    NimbleX
    PCLinuxOS
    Sabayon
    SimplyMEPIS
    Xubuntu

    Entire List

     

    Services
    Web Calendar
    Linux Licenses

    Advertise at LinuxLinks.com

     

    Latest Portal Pages
    Mixxx
    energyXT2
    GRASS
    uDig
    QGIS
    gretl
    SPSS

     

    Add Link | Modify Link | About | FAQ | Guide | Privacy | Awards | Contact | SourceFiles.org
    Portal Version 0.7. Intel Blade.
    Comments to the webmaster are welcome.
    Copyright 2009 LinuxLinks.com All rights reserved.