Force Field Explorer 

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Visualization

bulletChimera "UCSF Chimera is a highly extensible, interactive molecular graphics program. It is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware."
bullet PyMol  "PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research."
bullet Rasmol / Protein Explorer  "Free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers."

Modeling Applications

bulletAPBS  "APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media."
bulletGAMESS  "The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is maintained by the members of the Gordon research group at Iowa State University."

Java

bulletJava 2 Platform, Standard Edition  "The premier solution for rapidly developing and deploying mission-critical, enterprise applications, J2SE provides the essential compiler, tools, runtimes, and APIs for writing, deploying, and running applets and applications in the Java programming language."   
bullet Java3D  "Developers can easily incorporate high-quality, scalable, platform-independent 3D graphics into Java technology-based applications and applets. The Java 3D application programming interface (API) provides a set of object-oriented interfaces that support a simple, high-level programming model."
bullet Beanshell  "BeanShell is a small, free, embeddable, Java source interpreter with object scripting language features, written in Java. BeanShell executes standard Java statements and expressions, in addition to obvious scripting commands and syntax."
bulletJava3D Community Site  "This is a community site put together by a bunch of enthusiastic volunteers to encourage more sharing of information among the members of the Java 3D community."

Washington University