In bio-catalysis, structural knowledge related to an enzyme and its substrate interactions complements and guides experimental investigations. These can be generated through computational techniques, such as homology or molecular modeling. For this type of computational work, a computer program developed for molecular modeling of proteins is required.
YASARA is a molecular-graphics, modeling and simulation program for Windows, Linux, MacOS and Android developed since 1993. With an intuitive user interface, photorealistic graphics and support for affordable virtual reality headsets, shutter glasses, auto stereoscopic shows and input devices, YASARA creates a new level of interaction with the ‘artificial reality’, that allows us to focus on our goal.
YASARA is powered by PVL (Portable Vector Language), a new development framework that gives performance way above traditional software. PVL allows us to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, making use of GPUs if available. We can push and pull molecules around and work with dynamic models instead of static pictures.
This server performs an energy minimization. We just have to enter our email address, upload our protein model in PDB format and click the ‘Submit’ button. The results will be placed in a public download area; therefore we do not submit confidential data. We can also use this functionality and much more on our own computer by using YASARA.
YASARA has gradually grown to an all-in-one solution that takes the steps from protein sequence to structure to function to drug design, and is nevertheless powerful enough to handle the large amounts of data required by structural and functional genomics projects in the bioinformatics field.
If we want to submit multiple structures, we have to wait until we receive the confirmation email before submitting the next structure. Then we can sort the results based on the growing number in the download path and retrieve them in the proper order. We get the best performance if we not only wait for the confirmation, but for the actual result before submitting the next job. The reason is that all jobs we submit while another job of ours is in the pipeline get decreased priority and has to wait until no more ‘first submissions’ are in the queue.
YASARA provides a number of features with unique properties:
- Molecular graphics with GPU shaders and tessellation
- Molecular movies and eLearning
- Molecular dynamics with 4 clicks
- Scientific reports with 4 clicks
- New force fields: YASARA, YAMBER, NOVA
- Fastest molecular dynamics algorithms for GPU and CPU
- Automatic force field parameter assignment for 98% of the PDB
- pH dependent hydrogen bonding networks
- NMR structure determination with 4 clicks
- Modeling and simulation on smartphones and tablets
- Interactive real-time surfaces
- Interactive small-molecule builder
- pH dependent typing of organic molecules
- MD simulation of membrane proteins with 4 clicks
- Small-molecule docking with 4 clicks
- Side-chain prediction
- Structure validation including ligands
- Multi-dimensional knowledge based potentials