Computational Antibody Papers
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2024-12-18
Focused learning by antibody language models using preferential masking of non-templated regions
- language models
- Novel masking scheme for antibody sequences with applications to Vh-Vl pairing and specificity prediction.
- Since antibodies have intrinsically biased mutation patterns in favor of CDRs, the authors questioned the canonical 15% uniform masking procedure in antibody language models.
- They focused the masking on the CDR3 regions during training which resulted in faster convergence.
- They tested pairing prediction of Vh/Vl and they noticed 60% random vs non-random pairing accuracy.
- Prost5 : novel language model using the FoldSeek structural representation to introduce structural dimension to the model.
- The foldseek 3Di representation is used to encode 3D protein structures as 1D token sequences, enabling seamless translation between amino acid sequences and structural representations.
- The model was fine-tuned on 17 million AlphaFoldDB structures using ProtT5 as a base, with bi-directional translation tasks to map between amino acid (AA) and 3Di sequences.
- ProstT5 achieves 3600-fold faster remote homology detection compared to AlphaFold-based methods, while maintaining near-experimental accuracy and improving fold classification tasks like CATH.
- ProstT5 embeddings outperform ProtT5, ESM-1b, and Ankh for structure-related tasks and show competitive performance in inverse folding, generating diverse sequences with preserved structural similarity. Though in most cases ProteinMPNN still performs better for inverse folding.
2024-12-18
IgBlend: Unifying 3D Structures and Sequences in Antibody Language Models
- language models
- nanobodies
- Novel language model for antibodies, blending sequence and structural information.
- The model encodes sequence ‘as usual’ and uses GVP-GNN (like esm-if) for structural representation. Only the three backbone atoms (C,N,Ca) are taken per residue to get the structural representation.
- The data is a mix of sequence data and X-ray structures. The sequence datasets were modeled using ImmuneBuilder to increase structural coverage.
- The model has an MLM objective on sequence & structure with three losses - sequence only, sequence + structure and structure only.
- On sequence infilling IgBLEND performs better than other methods (e.g. AbLang, Nanobert), though arguably CDR-H3 predictions look very ‘close’ across the board.
- On inverse folding the method performs quite a stretch better with large gaps in CDR-H3 with notable improvements for nanobodies - that other methods like ESM-IF or AntiFold did not handle natively.
- Novel algorithm to perform structural search of proteins and at the same time introduces an innovative way to encode protein structures
- It encodes protein structures as sequences over a 20-state 3Di alphabet, representing tertiary residue-residue interactions (Ca of neighboring residues) rather than backbone conformations, enabling faster sequence-based comparisons.
- The 3Di alphabet and substitution matrix were trained on the SCOPe40 dataset (~11k structures), which consists of manually classified single-domain protein structures clustered at 40% sequence identity.
- FoldSEEK is thousands of times faster than structural alignment tools like Dali, TM-align, and CE, being 184,600 times faster than Dali and 23,000 times faster than TM-align on the AlphaFoldDB.
- FoldSEEK achieves sensitivities of 86%, 88%, and 133% relative to Dali, TM-align, and CE, respectively, and ranks among the top tools in precision-recall benchmarks.
- FoldSEEK produces alignments with accuracy comparable to Dali and TM-align, is 15% more sensitive than CE, and excels in detecting homologous multi-domain structures efficiently.
2024-11-22
Prediction of Paratope–Epitope Pairs Using Convolutional Neural Networks
- binding prediction
- epitope prediction
- Novel epitope-paratope prediction method, ImaPEp.
- The method projects the epitope and paratope onto 2D images and then uses a ResNET to predict the interacting vs non-interacting pairs.
- Negative set was done by pairing non-cognate antibody-antigen pairs, rotations etc.
- The method was not benchmarked against epitope predictions tools, that arguably do not take pairs into account, but against docking tools, scoring 13 out of 18 methods tested.
2024-11-22
AlphaBind, a Domain-Specific Model to Predict and Optimize Antibody-Antigen Binding Affinity
- binding prediction
- language models
- AlphaBind, a deep learning model designed to optimize antibody sequences, by leveraging large-scale pre-trained affinity datasets and fine-tuning on experimental data.
- AlphaBind was pre-trained on a dataset of 7.5 million antibody-antigen affinity measurements, which includes data from yeast display systems and diverse antibody libraries obtained from multiple experimental sources, focusing on quantitative affinity measurements.
- The model utilizes transformer-based architecture with protein sequence embeddings generated using ESM-2nv (Evolutionary Scale Model) embeddings. The model consists of 4 attention heads, 7 layers, and about 15 million parameters.
- The model fine-tunes on specific antibody-antigen systems using AlphaSeq data, then performs stochastic greedy optimization by generating sequence mutations (using ESM-2nv logits) to explore sequence space and predict binding affinity. This process generates thousands of candidate sequences, which are filtered based on affinity predictions and developability metrics before in vitro validation.
- The novel sequences based on three systems were verified in experimentally.
2024-11-22
Structure Language Models for Protein Conformation Generation
- generative methods
- language models
- non-antibody stuff
- Novel model for sampling the structural space of proteins - applied to nanobodies.
- Protein structures are encoded into latent tokens using a discrete variational auto-encoder (dVAE), which captures residue-level local geometric features in a roto-translation invariant manner.
- The model combines a dVAE encoder-decoder with a Structure Language Model (SLM) to model sequence-to-structure relationships.
- One can sample alternate conformations by providing an amino acid sequence as input and use the SLM to generate latent tokens representing potential conformations. Decode these latent tokens back into 3D structures using the dVAE decoder to generate diverse structural ensembles.
- Altogether, though they develop ESMdiff in the context of the paper, it is rather the structural language in the context of the broader framework of language models that forms the core of the message, rather than any single method.
- The model was evaluated on tasks like generating equilibrium dynamics, fold-switching, and intrinsically disordered proteins, using metrics like JS-divergence, TM-score, and RMSD. It outperformed existing methods in speed and accuracy, generating structures 20-100× faster.
2024-11-22
Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models
- developability
- Novel method for antibody library design.
- Given a structural complex, they employ AntiFold and Protbert to explore the ‘fitness’ space, to generate a set of mutants.
- To achieve multi-parameter optimization they use linear programming, rather than neural nets that are in vogue.
- The method was not validated experimentally, rather using computational proxies.
2024-11-14
Computational design of developable therapeutic antibodies: efficient traversal of binder landscapes and rescue of escape mutations
- developability
- binding prediction
- Pilot single-shot computational antibody design, where known binders were taken and new ones computationally generated on their basis, maintaining binding with a good developability profile.
- The pipeline starts with known binders to the SARS-CoV-2 RBD
- Novel binders were generated using a combination of computational approaches, including: Observed Antibody Space (OAS): Paired and unpaired sequences from the OAS dataset to identify antibody candidates within a certain edit distance from the starting antibodies. Inverse Folding Model (AbMPNN):generated new antibody sequences maintaining structural features compatible with binding to the SARS-CoV-2 RBD. ESM: guided the mutation of sequences to retain or improve binding affinity while enhancing developability.
- The developability properties were assessed using Rosetta scoring to evaluate antibody stability and interface energetics, alongside TAP.
- Experimental methods for screening included size-exclusion chromatography (SEC) to assess aggregation propensity and differential scanning fluorimetry (DSF) for thermal stability. Antibodies that passed these criteria were deemed suitable for development.
- Success rate of the method: The pipeline demonstrated a success rate of 54% for generating binding antibodies that retained affinity against escape mutations on the SARS-CoV-2 RBD.
- Authors tested RFDiffusion for the design task but with poor success rate - albeit not the antibody-fine tuned version it appears, that should work better.
2024-11-14
Transfer learning to leverage larger datasets for improved prediction of protein stability changes
- non-antibody stuff
- developability
- Novel method to predict stability of proteins, based on ProteinMPNN.
- The method employs ProteinMPNN embeddings with a stability prediction module to gauge the effect of single point mutations on protein stability.
- The Stability prediction module is composed of the light attention module (that figures out which parts of the embeddings should be upvoted) followed by shallow multi layer perceptron.
- For training/evaluation they employed Megascale and Fireprot datasets with measured protein stability data. Though after much pre-processing because the original datasets either contained many unreliable data points, or there was a risk that the mutations would change the structure too much.
- Ablations show that all the elements of the network are important and bring something to the prediction, with ProteinMPNN having quite some predictive power out-of-the box.