MARA is here to aid in your Bioinformatics research projects
In the ever-evolving landscape of bioinformatics, software tools play a pivotal role in translating complex biological data into meaningful insights. In this blog post, we’ll delve into the functionalities and innovations behind MARA, highlighting how it stands out in the crowded field of bioinformatics tool hubs. We’ll explore its capabilities for analyzing your data and the practical applications that make it a valuable asset for researchers. Whether you're a seasoned bioinformatician or just beginning to navigate the world of molecular data, MARA promises to be a game-changer in your toolkit.
Build custom tools, query databases, easily interconvert files
Leverage our custom-built tools (and build your own) to access and interact with a broad range of public data sources tailored to your research needs. Our platform enables you to query comprehensive databases, allowing you to locate relevant papers, explore specific topics, and efficiently retrieve citations from a wealth of published journals.
In addition, MARA directly imports and exports many file formats and supports the direct interconnection with local databases, including but not limited to PDB (Protein Data Bank) files, SDF (Structure Data File) files, and SMILES (Simplified Molecular Input Line Entry System) strings. Further, you can import data from your own servers directly into MARA, where it will be organized and stored as a data table for in-depth analysis. Contact our sales team at hello@nanome.ai for more information about Enterprise options.
Workflow
- Download PDB structure by PDB ID
- Find similar proteins based on amino acid sequence
- Return table with sequence identity of results
- Perform multiple sequence alignment
- View variations in sequence
- Download homologue and introduce mutation
- Apply rotamer library to a key residue
- View rotamers and change representation/color with natural language
The workflow below is completed without any prior data existing. MARA is employed to string together multiple tools and processes to allow you more time in the lab or focusing on other tasks.
Find Similar Proteins Based on AA Sequence
MARA uses reasoning to decide which paths to take with the tools available. This enables MARA to use a prompt such as “use the amino acid sequence of 2ONH to find similar proteins” to decide that a pdb file needs to be downloaded from RCSB PDB, converted to fasta, and that we want to find proteins with a similar sequence.
MARA allows users to interact with many file types directly in MARA, reducing the number of applications required to toggle between, saving your valuable time.
Download PDB files for most similar sequences
MARA directly reads data tables and extracts important information to complete tasks. A prompt of “download pdb for the top two hits with similarity < 1“ is then followed by MARA reading the data table, internally sorting, and downloading the pdb files for the top two hits with a sequence identity < 1%.
Introduce mutations and produce rotamer libraries using natural language
Since MARA understands what tools require specific files, a simple prompt such as “download pdb for 2ONH and make a mutation at residue 345 to ILE” is all that is required to produce a new pdb file with a required mutation. Rotamer libraries are easily added by simply requesting MARA to create a new file with a rotamer library at a key residue.
Summary
In summary, using MARA for a bioinformatics workflow transcends mere data handling; it is the alchemy of transforming raw information into profound knowledge. This knowledge can ignite groundbreaking scientific discoveries and foster advancements in medicinal chemistry, agriculture, environmental science, and energy storage. Within this intricate process, MARA emerges as an indispensable tool. MARA streamlines data interpretation and accelerates the journey from raw data to actionable insights, making it an essential component in the modern bioinformatician’s arsenal.
Want to try MARA out yourself? Click here to begin with 50 free credits.