ProteinMPNN
ProteinMPNN
Version: 2
NvidiaLast updated May 2025
ProteinMPNN (Protein Message Passing Neural Network) is a cutting-edge, deep learning-based, graph neural network designed to predict amino acid sequences for given protein backbones. This network leverages evolutionary, functional, and structural information to generate sequences that are likely to fold into the desired 3D structures. The input to the neural network is a 3D structure of a protein in PDB format, and the output is the amino-acid sequence in Multi-FASTA format. ProteinMPNN is one of many NIMs that you can apply to tasks in biosciences and drug discovery. NIMs make it easy to chain models together to develop a complete in silico drug discovery pipeline. For example, you can use a ProteinMPNN NIM as a subsequent step after RFdiffusion generative model NIM in order to determine possible amino acid sequence. ProteinMPNN is available as an NVIDIA NIM™ microservice, part of NVIDIA AI Enterprise . NVIDIA NIM offers prebuilt containers for large language models (LLMs) that can be used to develop chatbots, content analyzers—or any application that needs to understand and generate human language. Each NIM consists of a container and a model and uses a CUDA-accelerated runtime for all NVIDIA GPUs, with special optimizations available for many configurations. NVIDIA NIM is the fastest way to achieve accelerated generative AI inference at scale and has been benchmarked to have up to 2.6x improved throughput latency. NVIDIA AI Enterprise
NVIDIA AI Enterprise is an end-to-end, cloud-native software platform that accelerates data science pipelines and streamlines development and deployment of production-grade co-pilots and other generative AI applications. Easy-to-use microservices provide optimized model performance with enterprise-grade security, support, and stability to ensure a smooth transition from prototype to production for enterprises that run their businesses on AI.

Intended Use

Primary Use Cases

List the model's use cases in 1-2 paragraphs. You can add more descriptions as needed. Example: The model is intended for broad commercial and research use in English. The model provides uses for general purpose AI systems and applications which require:
  1. Memory/compute constrained environments
  2. Latency bound scenarios
  3. Strong reasoning (especially code, math and logic)
Our model is designed to accelerate research on language and multimodal models, for use as a building block for generative AI powered features.

Out-of-Scope Use Cases

Describe the use case that the model is not designed for. Example: Our models are not specifically designed or evaluated for all downstream purposes. Developers should consider common limitations of language models as they select use cases, and evaluate and mitigate for accuracy, safety, and fairness before using within a specific downstream use case, particularly for high-risk scenarios. Developers should be aware of and adhere to applicable laws or regulations (including privacy, trade compliance laws, etc.) that are relevant to their use case.

Responsible AI Considerations

Describe how the model is trained to meet the responsible AI considerations. Example: Like other language models, the Phi family of models can potentially behave in ways that are unfair, unreliable, or offensive. Some of the limiting behaviors to be aware of include:
  • Quality of Service: The Phi models are trained primarily on English text and some additional multilingual text. Languages other than English will experience worse performance as well as performance disparities across non-English. English language varieties with less representation in the training data might experience worse performance than standard American English.
  • Multilingual performance and safety gaps: We believe it is important to make language models more widely available across different languages, but the Phi 3 models still exhibit challenges common across multilingual releases. As with any deployment of LLMs, developers will be better positioned to test for performance or safety gaps for their linguistic and cultural context and customize the model with additional fine-tuning and appropriate safeguards.
  • Representation of Harms & Perpetuation of Stereotypes: These models can over- or under-represent groups of people, erase representation of some groups, or reinforce demeaning or negative stereotypes. Despite safety post-training, these limitations may still be present due to differing levels of representation of different groups, cultural contexts, or prevalence of examples of negative stereotypes in training data that reflect real-world patterns and societal biases.
  • Inappropriate or Offensive Content: These models may produce other types of inappropriate or offensive content, which may make it inappropriate to deploy for sensitive contexts without additional mitigations that are specific to the use case.
  • Information Reliability: Language models can generate nonsensical content or fabricate content that might sound reasonable but is inaccurate or outdated.
  • Limited Scope for Code: Majority of Phi-3 training data is based in Python and use common packages such as "typing, math, random, collections, datetime, itertools". If the model generates Python scripts that utilize other packages or scripts in other languages, we strongly recommend users manually verify all API uses.
  • Long Conversation: Phi-3 models, like other models, can in some cases generate responses that are repetitive, unhelpful, or inconsistent in very long chat sessions in both English and non-English languages. Developers are encouraged to place appropriate mitigations, like limiting conversation turns to account for the possible conversational drift.
Developers should apply responsible AI best practices, including mapping, measuring, and mitigating risks associated with their specific use case and cultural, linguistic context. Phi-3 family of models are general purpose models. As developers plan to deploy these models for specific use cases, they are encouraged to fine-tune the models for their use case and leverage the models as part of broader AI systems with language-specific safeguards in place. Important areas for consideration include:
  • Allocation: Models may not be suitable for scenarios that could have consequential impact on legal status or the allocation of resources or life opportunities (ex: housing, employment, credit, etc.) without further assessments and additional debiasing techniques.
  • High-Risk Scenarios: Developers should assess the suitability of using models in high-risk scenarios where unfair, unreliable or offensive outputs might be extremely costly or lead to harm. This includes providing advice in sensitive or expert domains where accuracy and reliability are critical (ex: legal or health advice). Additional safeguards should be implemented at the application level according to the deployment context.
  • Misinformation: Models may produce inaccurate information. Developers should follow transparency best practices and inform end-users they are interacting with an AI system. At the application level, developers can build feedback mechanisms and pipelines to ground responses in use-case specific, contextual information, a technique known as Retrieval Augmented Generation (RAG).
  • Generation of Harmful Content: Developers should assess outputs for their context and use available safety classifiers or custom solutions appropriate for their use case.
  • Misuse: Other forms of misuse such as fraud, spam, or malware production may be possible, and developers should ensure that their applications do not violate applicable laws and regulations.

Training Data

Describe what data was used for the training of the model. Example: Our training data includes a wide variety of sources, totaling 4.9 trillion tokens (including 10% multilingual), and is a combination of
  1. Publicly available documents filtered rigorously for quality, selected high-quality educational data, and code;
  2. Newly created synthetic, “textbook-like” data for the purpose of teaching math, coding, common sense reasoning, general knowledge of the world (science, daily activities, theory of mind, etc.);
  3. High quality chat format supervised data covering various topics to reflect human preferences on different aspects such as instruct-following, truthfulness, honesty and helpfulness.
We are focusing on the quality of data that could potentially improve the reasoning ability for the model, and we filter the publicly available documents to contain the correct level of knowledge. As an example, the result of a game in premier league in a particular day might be good training data for frontier models, but we need to remove such information to leave more model capacity for reasoning for the small size models. More details about data can be found in the Phi-3 Technical Report .
ProteinMPNN NIM is optimized to run best on the following compute:
GPUTotal GPU memoryAzure VM compute#GPUs on VMLink
A10080Standard_NC24ads_A100_v41link
A100160Standard_NC48ads_A100_v42link
A100320Standard_NC96ads_A100_v44link
A100640STANDARD_ND96AMSR_A100_V48link
H10094STANDARD_NC40ADS_H100_V51link
H100188STANDARD_NC80ADIS_H100_V52link
Model Specifications
LicenseCustom
Last UpdatedMay 2025
PublisherNvidia