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countless pages of doc- umentation, you can simply run one of the interactive tutorials, where our mascott Yami Yet Another Scientific Artificial Reality Application (on the right) shows you B I O S C I E N C E S what to do. These tutorials are not limited to YASARA is a molecular-graphics, modeling and simu- YASARA specific topics, lation application for Windows, Linux and MacOSX, that you can also learn Watching Nature@Work makes it really easy to answer your questions. With an about modeling and molecular dynamics simulations in intuitive user interface and support general, without having to book expensive courses. Cre- for affordable stereoscopic dis- ate your own YASARA Movies for virtually any purpose, plays, YASARA creates a new level like a multimedia presentation to accompany your next of interaction with the 'artificial re- talk or teach a course. Movies can be encoded (e.g. for ality', that allows you to focus on YouTube) or played back interactively in real-time using your goal and forget about the details of the program.

the free YASARA View, so that everyone can watch your

work. See www.yasara.org/movies. These are YASARA's six strongest points, that help our

5) Completeness: YASARA offers the majority of func- w users most when compared to other products: tions ever needed, from molecular graphics to molecular 1) Innovation: YASARA includes dozens of helpful fea- modeling, MD simulations, docking and protein structure w tures that accelerate your research and cannot be found prediction, all at the touch of a button, with YASARA tak- in any other software on the market. See ing care of the details: www.yasara.org/products. www.yasara.org/products for a list of functions you

w 6) Price: Being committed to science - not shareholders - might currently miss. and thanks to our efficient development process with 2) Accuracy: A major part of our research is dedicated close academic ties to the CMBI at the Radboud Universi- .

Y to the development of new force fields for increasingly ty Nijmegen, the Netherlands, we can offer you YASARA accurate molecular simulations and energy calculations, either for free including support (the starter edition A including fully automatic setup and parameter assignment YASARA View) or for a tiny fraction of what feature- for the entire PDB. See www.yasara.org/science- complete molecular modeling software used to cost. S news for a list of articles. YASARA is so affordable that we even dare to list our prices on the website www.yasara.org/products. A 3) Performance: YASARA is developed with our own custom compiler 'PVL' (Portable Vector Language) that As a YASARA user, you are not limited to the role of a R fully exploits the power of today's CPUs (Multi-cores/ consumer, but encouraged to actively participate in de- MMX/SSE1-4/AVX) and GPUs, delivering the highest velopment. If you contribute macros, movies, Python plug- A performance for applications like molecular dynamics ins, or just feedback, you receive credits that in turn give

. and molecular graphics, see www.yasara.org/bench- you free access to all stages of YASARA. These contrib- o marks. PVL enables true interactive real-time simulations uted add-ons to YASARA are generally released as open on standard PCs, you can push and pull your molecules source, so that you can freely share your work. r around and work with dynamic models instead of static

g pictures. Cross-eyed stereo screenshot of a myosin model. Particle Mesh Ewald longrange electrostatics. YASARA Cross-eyed stereo screenshot of an interactive real-time Products Dynamics is not a "black box" with input and output molecular dynamics simulation. files, but shows the MD simulation in real-time on screen. There are four different stages of YASARA for Win- You can fully interact with the scene, and pull atoms or dows, Linux and MacOSX, aimed at increasingly compli- whole molecules around. cated fields of application. A certain stage contains the features of all the previous stages, plus a number of ad- Stage IV: YASARA Structure ditional functions to tackle a wider range of scientific questions. YASARA Structure finally contains all the functions needed to predict and validate macromolecular struc- Stage I: YASARA View - Free for everyone tures, including ligand docking, homology modeling and YASARA View is available for free and contains the highly accurate force fields basic functions you need to explore and analyze macro- with knowledge-based poten- molecular structures interac- tials for high-resolution refine- tively, comparable to other ment. An add-on module for NMR structure determination molecule viewers. As a bonus, is also available. you get YASARA's innovative 3D graphics engine, which is The WHAT IF / YASARA Twinset up to 35 times faster than what you usually know from OpenGL-based applications, you can load multiple struc- With over 2000 citations, the WHAT IF molecular tures at the same time, create publication-quality ray- modeling program (www.cmbi.ru.nl/whatif) has been traced images including labels, and program your own among the pioneers in the field since 1987. Apart from a macros and Python scripts. Included is YASARA Movie, a wide range of general molecular modeling functions, player for multimedia presentations and tutorials created WHAT IF provides today's most extensive structure vali- with any of the higher stages. Download today! dation capabilities, that uncover each and Stage II: YASARA Model every flaw in molecular models, ranging YASARA Model contains all the functions you need from homology models to analyze and model macromolecules in a production built in silico to real environment. This includes un- structures solved ex- limited undo/redo, macro perimentally. The Twin- recorder and quad-buffered set is a customized joint-distribution of WHAT IF and stereo. You can load thousands YASARA, where WHAT IF inherits YASARA's user inter- of structures at the same time, face, graphics engine, macro language, unlimited move them around independently and create multimedia undo/redo etc., so that its functions become easily acces- presentations (YASARA Movies). These movies can be sible. played back with all stages of YASARA, including the free YASARA View. Modeling and 3D Stereo Equipment Stage III: YASARA Dynamics YASARA supports a number of innovative and affordable de- YASARA Dynamics adds support for molecular sim- vices created by ulations. In addition to YASARA's own force fields other companies (NOVA, YAMBER) you can use to build your own other well known MD force 3D molecular fields like AMBER, and run ac- modeling labora- curate all-atom MD simula- tory. tions in aqueous solution with