Tokenizing Loops of Antibodies | Paper Citation Record

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This paper cites write newline.

Tokenizing Loops of Antibodies write newline

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This paper cites @esa (Ref.

Tokenizing Loops of Antibodies @esa (Ref

Reference 2

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This paper cites an unresolved cited work.

Tokenizing Loops of Antibodies Unresolved cited work

Reference 3

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This paper cites an unresolved cited work.

Tokenizing Loops of Antibodies Unresolved cited work

Reference 4

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Observation 15ea0a7c-dccd-4631-a1f1-03112843c6e8 · outbound

This paper cites Pyigclassify: a database of antibody cdr structural classifications.

Tokenizing Loops of Antibodies Pyigclassify: a database of antibody cdr structural classifications

Reference 5

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This paper cites Rosettaantibodydesign (rabd): A general framework for computational antibody design.

Tokenizing Loops of Antibodies Rosettaantibodydesign (rabd): A general framework for computational antibody design

Reference 6

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This paper cites Can alphafold2 predict the impact of missense mutations on structure? Nature structural & molecular biology, 29 0 (1): 0 1--2, 2022.

Tokenizing Loops of Antibodies Can alphafold2 predict the impact of missense mutations on structure? Nature structural & molecular biology, 29 0 (1): 0 1--2, 2022

Reference 7

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Observation 15457659-9a6d-456d-8a51-6fc8950a7ae0 · outbound

This paper cites Canonical structures for the hypervariable regions of immunoglobulins.

Tokenizing Loops of Antibodies Canonical structures for the hypervariable regions of immunoglobulins

Reference 8

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Observation 6422bdd0-f164-4546-b2bd-b8ddedfabe24 · outbound

This paper cites Antibodies to watch in 2025.

Tokenizing Loops of Antibodies Antibodies to watch in 2025

Reference 9

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Observation 895db7d5-aa18-4986-aad7-53d4f6ab45eb · outbound

This paper cites scgpt: toward building a foundation model for single-cell multi-omics using generative ai.

Tokenizing Loops of Antibodies scgpt: toward building a foundation model for single-cell multi-omics using generative ai

Reference 10

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Observation 0f3f1e12-4772-479c-b2ab-193343c8129f · outbound

This paper cites Robust deep learning--based protein sequence design using proteinmpnn.

Tokenizing Loops of Antibodies Robust deep learning--based protein sequence design using proteinmpnn

Reference 11

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This paper cites Bert: Pre-training of deep bidirectional transformers for language understanding.

Tokenizing Loops of Antibodies Bert: Pre-training of deep bidirectional transformers for language understanding

Reference 12

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Observation 4e040541-717b-4772-a9fd-cc610f6b8a70 · outbound

This paper cites An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale.

Tokenizing Loops of Antibodies An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

Reference 13

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Observation 482b0a82-2309-4a44-9749-4b16e6fbaa71 · outbound

This paper cites Inverse folding for antibody sequence design using deep learning.

Tokenizing Loops of Antibodies Inverse folding for antibody sequence design using deep learning

Reference 14

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Observation f6f93e0b-73b2-43c2-9a66-9d2baab9f269 · outbound

This paper cites Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins.

Tokenizing Loops of Antibodies Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins

Reference 15

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Observation 2d65c5c6-ee72-4375-a711-ca2fefebb110 · outbound

This paper cites Computational design of therapeutic antibodies with improved developability: efficient traversal of binder landscapes and rescue of escape mutations.

Tokenizing Loops of Antibodies Computational design of therapeutic antibodies with improved developability: efficient traversal of binder landscapes and rescue of escape mutations

Reference 16

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Observation d94a97b3-6723-40c7-b586-a975a2eca3e7 · outbound

This paper cites Anarci: antigen receptor numbering and receptor classification.

Tokenizing Loops of Antibodies Anarci: antigen receptor numbering and receptor classification

Reference 17

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Observation 1f359507-b432-4105-b225-a9eb247928b0 · outbound

This paper cites Sabdab: the structural antibody database.

Tokenizing Loops of Antibodies Sabdab: the structural antibody database

Reference 18

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Observation 4d034ce8-daaf-48e0-b782-5b2a1ebb4281 · outbound

This paper cites Esm cambrian: Revealing the mysteries of proteins with unsupervised learning, December 2024.

Tokenizing Loops of Antibodies Esm cambrian: Revealing the mysteries of proteins with unsupervised learning, December 2024

Reference 19

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Observation ac01931d-510a-4cfe-ba16-48ce60bd408c · outbound

This paper cites Learning universal representations of intermolecular interactions with atomica.

Tokenizing Loops of Antibodies Learning universal representations of intermolecular interactions with atomica

Reference 20

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Observation 662acbf4-46ea-4f11-8206-ead7d1e023ea · outbound

This paper cites Transitions of cdr-l3 loop canonical cluster conformations on the micro-to-millisecond timescale.

Tokenizing Loops of Antibodies Transitions of cdr-l3 loop canonical cluster conformations on the micro-to-millisecond timescale

Reference 21

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Observation 975c6a72-b95f-40d9-bf00-2fdaf7aecf42 · outbound

This paper cites Antibody cdr loops as ensembles in solution vs.

Tokenizing Loops of Antibodies Antibody cdr loops as ensembles in solution vs

Reference 22

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Observation 63085a26-d3ab-49d4-b515-35e154e37fb3 · outbound

This paper cites Lab-in-the-loop therapeutic antibody design with deep learning.

Tokenizing Loops of Antibodies Lab-in-the-loop therapeutic antibody design with deep learning

Reference 23

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Observation a521b982-7750-4655-81ac-14568a3f7ea6 · outbound

This paper cites Computing and visualizing dynamic time warping alignments in r: the dtw package.

Tokenizing Loops of Antibodies Computing and visualizing dynamic time warping alignments in r: the dtw package

Reference 24

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Observation 9f568afc-9c65-47e0-8bb6-4ec2dc37fb89 · outbound

This paper cites Simulating 500 million years of evolution with a language model.

Tokenizing Loops of Antibodies Simulating 500 million years of evolution with a language model

Reference 25

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Observation e134b0a3-6bc9-4c82-8c6a-94a5c0131d48 · outbound

This paper cites Bilingual language model for protein sequence and structure.

Tokenizing Loops of Antibodies Bilingual language model for protein sequence and structure

Reference 26

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Observation 7dbba74a-2602-4770-a18c-98fc1c77b5bf · outbound

This paper cites Efficient evolution of human antibodies from general protein language models.

Tokenizing Loops of Antibodies Efficient evolution of human antibodies from general protein language models

Reference 27

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Observation eb635c7b-f166-4fce-96f6-7078b0e599da · outbound

This paper cites AntiFold: Improved antibody structure-based design using inverse folding.

Tokenizing Loops of Antibodies AntiFold: Improved antibody structure-based design using inverse folding

Reference 28

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Observation 1fbe5ea0-7cf7-41f4-9e3d-b32bdb740b6d · outbound

This paper cites Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool.

Tokenizing Loops of Antibodies Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool

Reference 29

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This paper cites Learning inverse folding from millions of predicted structures.

Tokenizing Loops of Antibodies Learning inverse folding from millions of predicted structures

Reference 30

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Observation f1691765-a3c2-4389-bc8a-2fda61679356 · outbound

This paper cites Learning from Protein Structure with Geometric Vector Perceptrons.

Tokenizing Loops of Antibodies Learning from Protein Structure with Geometric Vector Perceptrons

Reference 31

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Observation 966ef8c6-3931-4b98-8554-346eefc5e7ce · outbound

This paper cites A penultimate classification of canonical antibody cdr conformations.

Tokenizing Loops of Antibodies A penultimate classification of canonical antibody cdr conformations

Reference 32

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Observation a3a56e91-3b51-459a-a665-7b7a3fe035e7 · outbound

This paper cites Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody de loop for antibody-antigen binding.

Tokenizing Loops of Antibodies Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody de loop for antibody-antigen binding

Reference 33

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Observation db47e2ce-a6e1-4aca-a11f-87e58b23fc8f · outbound

This paper cites Large scale paired antibody language models.

Tokenizing Loops of Antibodies Large scale paired antibody language models

Reference 34

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Observation 3ac4225b-3563-4582-a199-2ba42374b846 · outbound

This paper cites Protein function prediction as approximate semantic entailment.

Tokenizing Loops of Antibodies Protein function prediction as approximate semantic entailment

Reference 35

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This paper cites Stcrdab: the structural t-cell receptor database.

Tokenizing Loops of Antibodies Stcrdab: the structural t-cell receptor database

Reference 36

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This paper cites Prosst: Protein language modeling with quantized structure and disentangled attention.

Tokenizing Loops of Antibodies Prosst: Protein language modeling with quantized structure and disentangled attention

Reference 37

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This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

Tokenizing Loops of Antibodies Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 38

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Observation 079507c4-89f1-4acf-ac42-5c109fd193db · outbound

This paper cites Do antibody cdr loops change conformation upon binding? In MAbs, volume 16, pp.\ 2322533.

Tokenizing Loops of Antibodies Do antibody cdr loops change conformation upon binding? In MAbs, volume 16, pp.\ 2322533

Reference 39

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This paper cites Scop: a structural classification of proteins database.

Tokenizing Loops of Antibodies Scop: a structural classification of proteins database

Reference 40

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This paper cites Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space.

Tokenizing Loops of Antibodies Co-optimization of therapeutic antibody affinity and specificity using machine learning models that generalize to novel mutational space

Reference 41

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This paper cites UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.

Tokenizing Loops of Antibodies UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Reference 42

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This paper cites Pfam: The protein families database in 2021.

Tokenizing Loops of Antibodies Pfam: The protein families database in 2021

Reference 43

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Observation 52beae30-e624-45ea-a0ee-6bb83ec48872 · outbound

This paper cites A new clustering of antibody cdr loop conformations.

Tokenizing Loops of Antibodies A new clustering of antibody cdr loop conformations

Reference 44

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This paper cites Proteingym: Large-scale benchmarks for protein fitness prediction and design.

Tokenizing Loops of Antibodies Proteingym: Large-scale benchmarks for protein fitness prediction and design

Reference 45

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This paper cites Length-independent structural similarities enrich the antibody cdr canonical class model.

Tokenizing Loops of Antibodies Length-independent structural similarities enrich the antibody cdr canonical class model

Reference 46

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Observation a18d5901-43a5-4269-a8c7-48f161e2e3e7 · outbound

This paper cites Observed antibody space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences.

Tokenizing Loops of Antibodies Observed antibody space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences

Reference 47

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This paper cites Addressing the antibody germline bias and its effect on language models for improved antibody design.

Tokenizing Loops of Antibodies Addressing the antibody germline bias and its effect on language models for improved antibody design

Reference 48

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This paper cites Classification schemes for protein structure and function.

Tokenizing Loops of Antibodies Classification schemes for protein structure and function

Reference 49

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This paper cites Using alphafold to predict the impact of single mutations on protein stability and function.

Tokenizing Loops of Antibodies Using alphafold to predict the impact of single mutations on protein stability and function

Reference 50

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This paper cites QuaterNet: A Quaternion-based Recurrent Model for Human Motion.

Tokenizing Loops of Antibodies QuaterNet: A Quaternion-based Recurrent Model for Human Motion

Reference 51

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This paper cites Structural classification of cdr-h3 in antibodies.

Tokenizing Loops of Antibodies Structural classification of cdr-h3 in antibodies

Reference 52

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This paper cites Prosite, a protein domain database for functional characterization and annotation.

Tokenizing Loops of Antibodies Prosite, a protein domain database for functional characterization and annotation

Reference 53

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This paper cites Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.

Tokenizing Loops of Antibodies Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Reference 54

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Tokenizing Loops of Antibodies Saprot: Protein language modeling with structure-aware vocabulary

Reference 55

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Tokenizing Loops of Antibodies Semantical and geometrical protein encoding toward enhanced bioactivity and thermostability

Reference 56

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This paper cites Structural diversity in a human antibody germline library.

Tokenizing Loops of Antibodies Structural diversity in a human antibody germline library

Reference 57

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This paper cites Somatic generation of antibody diversity.

Tokenizing Loops of Antibodies Somatic generation of antibody diversity

Reference 58

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Tokenizing Loops of Antibodies Neural discrete representation learning

Reference 59

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Observation 5810a99a-9969-4303-a0a4-2c8d5402e346 · outbound

This paper cites Fast and accurate protein structure search with foldseek.

Tokenizing Loops of Antibodies Fast and accurate protein structure search with foldseek

Reference 60

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Observation 53edb2e4-78d9-4231-a8b4-cb043e8fbfcd · outbound

This paper cites Learning Hierarchical Protein Representations via Complete 3D Graph Networks.

Tokenizing Loops of Antibodies Learning Hierarchical Protein Representations via Complete 3D Graph Networks

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This paper cites Scalop: sequence-based antibody canonical loop structure annotation.

Tokenizing Loops of Antibodies Scalop: sequence-based antibody canonical loop structure annotation

Reference 62

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Observation dde90299-22ff-4a8d-9daf-61d87061e392 · outbound

This paper cites Comparative analysis of the cdr loops of antigen receptors.

Tokenizing Loops of Antibodies Comparative analysis of the cdr loops of antigen receptors

Reference 63

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This paper cites Diversity in the cdr3 region of vh is sufficient for most antibody specificities.

Tokenizing Loops of Antibodies Diversity in the cdr3 region of vh is sufficient for most antibody specificities

Reference 64

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Observation 75020afd-20c1-46b2-8a52-b41458d78e64 · outbound

This paper cites Masked inverse folding with sequence transfer for protein representation learning.

Tokenizing Loops of Antibodies Masked inverse folding with sequence transfer for protein representation learning

Reference 65

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This paper cites Protein Structure Tokenization: Benchmarking and New Recipe.

Tokenizing Loops of Antibodies Protein Structure Tokenization: Benchmarking and New Recipe

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This paper cites Fast and Accurate Antibody Sequence Design via Structure Retrieval.

Tokenizing Loops of Antibodies Fast and Accurate Antibody Sequence Design via Structure Retrieval

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This paper cites Protein Representation Learning by Geometric Structure Pretraining.

Tokenizing Loops of Antibodies Protein Representation Learning by Geometric Structure Pretraining

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This paper cites Benchmark for antibody binding affinity maturation and design.

Tokenizing Loops of Antibodies Benchmark for antibody binding affinity maturation and design

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