MassiveFold: Revolutionizing Protein Structure Prediction with Optimized AlphaFold

MassiveFold: Customizable version of AlphaFold reduces protein structure prediction time from months to hours

Scientists from Université de Lille, France, Linköping University, Sweden, and collaborating institutions have introduced MassiveFold, a new version of AlphaFold that dramatically reduces computing time for protein structure predictions from months to hours. Protein structural prediction space is in a golden era of advancement, thanks to AI and machine learning tools. Biotechnology research heavily relies on discovering the correct protein structure to perform the desired task, with implications for just about any industry that interacts with biotechnology, from food to pharmaceuticals, fashion to biofuel, laundry detergent to agriculture, and seemingly everything in between. DeepMind's AlphaFold and the AlphaFold Protein Structure Database have been major contributors. Initially trained for single protein chains, AlphaFold has since gone beyond this, showing high levels of accuracy in modeling complex protein assemblies during the recent CASP15-CAPRI round of blind structure prediction. CASP (Critical Assessment of Structure Prediction) and CAPRI (Critical Assessment of Predicted Interactions) are two blinded benchmarks for protein prediction models to test their accuracy. Classically solved protein structures are chosen, and prediction tools are only given the amino acid sequences to work with. The closer a prediction model folding is to the actual structure, the higher the score. In a study titled "MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling," published in Nature Computational Science, the team introduces MassiveFold, an optimized and customizable version of AlphaFold that significantly enhances protein structure prediction capabilities. Comparative analyses showed that MassiveFold could produce good models for several CASP15 targets, sometimes outperforming the recently published AlphaFold3. Depending on the target, either MassiveFold or AlphaFold3 produced the best models, suggesting tradeoffs in prediction strategies. In the future, these strategies are likely to be integrated. MassiveFold significantly reduces computing time for protein structure predictions (from months to hours). This efficiency enables researchers to obtain results more rapidly, accelerating advancements in protein modeling and related scientific fields. Previously, massive sampling within AlphaFold has been used to generate a large number of protein structure predictions to explore a wide range of possible conformations, which enhances the ability to model protein assemblies more accurately. These massive sampling tasks take intense computational resources beyond what many research teams have available. MassiveFold addresses the challenges of high GPU resource demands and data storage that traditional AlphaFold applications face. Its ability to run predictions in parallel makes it practical even with limited computational resources. MassiveFold is also scalable and customizable, capable of running on anything from a single computer to a large GPU infrastructure. This flexibility allows it to fully benefit from all available computing nodes, making it accessible to a wide range of research environments. According to the study, the program is easy to use and install, requiring only a simple command line with a JSON parameter file. Its open-source availability to researchers encourages collaboration and further development within the scientific community, likely pushing the boundaries of what we can expect from clinical research and the biotech industry for many years to come.

MassiveFold advances protein structure prediction with efficient parallel processing

By Dr. Sushama R. Chaphalkar, PhD.Reviewed by Susha Cheriyedath, M.Sc.Nov 12 2024 With MassiveFold, scientists have unlocked AlphaFold's full potential, making high-confidence protein predictions faster and more accessible, fueling breakthroughs in biology and drug discovery. Brief Communication: MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling. Image Credit: Shutterstock AI In a recent study published in the journal Nature Computational Science, researchers from France developed MassiveFold, an enhanced version of AlphaFold tailored specifically for parallel processing. They aimed to reduce the prediction time for protein structures from months to hours. They found that MassiveFold efficiently enhanced structural modeling for proteins and protein assemblies while lowering computational costs, increasing prediction quality, and being scalable across various hardware setups. Background AlphaFold and the AlphaFold Protein Structure Database have transformed access to protein structure predictions, enabling modeling of both single chains and complex protein assemblies. However, despite the advantages of extensive sampling with AlphaFold, it remains computationally demanding and time-consuming. Massive sampling has been shown to reveal structural diversity and conformational variability in monomers and protein complexes, including intricate assemblies like nanobody complexes and antigen-antibody interactions. But this high sampling, while improving prediction accuracy, comes with major challenges in terms of GPU demand and long processing times. Specifically, AlphaFold's high graphics processing unit (GPU) demands and its inability to run in parallel create practical limitations. Standard AlphaFold-Multimer runs, particularly for large assemblies, often exceed the GPU cluster times set by computing infrastructures, hindering the completion of complex predictions. This makes AlphaFold's full potential challenging to realize within existing GPU resource constraints, which motivates the development of more efficient solutions for both single-chain and complex structural predictions. To address these challenges, researchers in the present study developed MassiveFold, a parallelized, customizable version of AlphaFold that distributes computing tasks across CPUs and GPUs to accelerate the prediction of protein structures. About the Study The provided inputs are the FASTA sequence(s) and parameter options for AFmassive or ColabFold. MassiveFold then runs the alignments on a CPU, producing multiple sequence alignments (MSAs) and divides the structure predictions for massive sampling in batches to be run on GPUs. After completion, MassiveFold automatically gathers all predictions, ranks them following the AlphaFold ranking confidence score, the predicted template modeling score (pTM) and interface predicted template modeling score (ipTM), and generates plots. MassiveFold version 1.2.5, developed in Bash and Python 3, combined AlphaFold's structure prediction capabilities with enhanced sampling through either AFmassive or ColabFold and optimized parallelization across central processing units (CPUs) and GPUs. Designed for flexibility, it enables users to adjust parameters like dropout rates, template usage, and recycling steps specified in a JavaScript Object Notation (JSON) file to increase structural diversity. The SLURM workload manager efficiently balances resources by adjusting batch sizes to ensure that jobs are completed within the designated time. The process included the following steps: (1) alignment generation on CPU cores (using JackHMMer, HHblits, or MMseqs2), (2) batch-based structure inference on GPUs, and (3) a final post-processing phase to rank predictions and generate plots. A time-saving feature is that precomputed alignments can also be reused. A script compiled results from multiple runs to consolidate rankings, as was done in the Critical Assessment of Structure Prediction 16 (CASP16) study, in which MassiveFold generated and ranked up to 8,040 predictions per target. Results and Discussion MassiveFold was found to effectively increase the diversity and confidence of protein structural predictions by adjusting sampling parameters, recycling, and dropout, thereby producing high-confidence structures for complex protein targets. For example, in the CASP15 H1140 target, MassiveFold could generate multiple diverse structures with high-confidence scores by extending sampling and using dropout without templates. Additionally, the use of extended recycling enhanced structural diversity, an approach validated with various CASP targets. Tests comparing MassiveFold to AlphaFold3 on CASP15 targets showed that MassiveFold's massive sampling approach produced good models for seven out of eight targets, while AlphaFold3 marginally outperformed MassiveFold in only three of the eight targets. Integration of AlphaFold3 into MassiveFold is planned to further enhance antibody-antigen prediction models, potentially combining the unique advantages of both tools. Conclusion In conclusion, MassiveFold demonstrates that overcoming the computational limitations of standard AlphaFold, particularly for large and complex protein assemblies, is achievable. MassiveFold optimized the use of GPU clusters for large-scale protein structure predictions, balancing GPU and CPU resources to handle massive sampling efficiently. This design not only enhanced structural diversity and reduced computational time but also allowed flexibility for both large multi-GPU setups and single-GPU environments. MassiveFold's capabilities make it well-suited for extensive exploration of the AlphaFold protein structure prediction landscape, promising significant applications in research and drug discovery.