Research graph
References from A comprehensive overview of recent advances in generative models for antibodies. Local targets link to admitted publications; unresolved targets remain external evidence.
Antibody-dependent cellular phagocytosis in antiviral immune responses
10.3389/fimmu.2019.00332 · 2019 · External reference
Role of antibody-dependent cell-mediated cytotoxicity in the efficacy of therapeutic anti-cancer monoclonal antibodies
10.1007/s10555-005-6192-2 · 2005 · External reference
10.1172/jci82695
10.1172/jci82695 · External reference
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Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery
10.1093/bib/bbac267 · 2022 · External reference
Phage Particles as Vaccine Delivery Vehicles: Concepts, Applications and Prospects
10.7314/apjcp.2015.16.18.8019 · 2015 · External reference
10.3390/antib8030044
10.3390/antib8030044 · External reference
Generative models for protein sequence modeling: recent advances and future directions
10.1093/bib/bbad358 · 2023 · External reference
Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures
10.52202/068431-0709 · 2022 · External reference
10.1016/j.gpb.2023.03.004
10.1016/j.gpb.2023.03.004 · External reference
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10.1016/j.cels.2023.10.001
10.1016/j.cels.2023.10.001 · External reference
Epitope-specific antibody design using diffusion models on the latent space of ESM embeddings
2023 · External reference
10.1016/j.sbi.2020.11.008
10.1016/j.sbi.2020.11.008 · External reference
Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
10.1371/journal.pcbi.1010271 · 2022 · External reference
Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies
10.1038/s41467-023-38063-x · 2023 · External reference
10.1038/s41586-023-06415-8
10.1038/s41586-023-06415-8 · External reference
10.1038/s41586-023-06728-8
10.1038/s41586-023-06728-8 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
2024 · External reference
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The mosaic puzzle of the therapeutic monoclonal antibodies and antibody fragments - A modular transition from full-length immunoglobulins to antibody mimetics
2022 · External reference
B cell receptor structure and effector function
10.1016/b978-012088451-3.50007-7 · 2006 · External reference
10.3390/antib8040055
10.3390/antib8040055 · External reference
10.1111/imr.12385
10.1111/imr.12385 · External reference
10.1101/2024.04.25.587828
10.1101/2024.04.25.587828 · External reference
Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design
10.1145/3580305.3599468 · 2023 · External reference
10.1101/2023.09.25.559190
10.1101/2023.09.25.559190 · External reference
10.1002/pro.4205
10.1002/pro.4205 · External reference
10.4049/jimmunol.1800708
10.4049/jimmunol.1800708 · External reference
SAbDab: the structural antibody database
10.1093/nar/gkt1043 · 2014 · External reference
10.1093/database/bay040
10.1093/database/bay040 · External reference
SACS--self-maintaining database of antibody crystal structure information
10.1093/bioinformatics/18.1.175 · 2002 · External reference
10.1093/bioinformatics/btaa739
10.1093/bioinformatics/btaa739 · External reference
sdAb-DB: the single domain antibody database
10.1021/acssynbio.8b00407 · 2018 · External reference
10.1109/bibm.2016.7822604
10.1109/bibm.2016.7822604 · External reference
MMseqs2 desktop and local web server app for fast, interactive sequence searches
10.1093/bioinformatics/bty1057 · 2019 · External reference
10.1016/j.molimm.2023.05.006
10.1016/j.molimm.2023.05.006 · External reference
Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures
10.1016/j.csbj.2023.11.056 · 2023 · External reference
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
10.1093/nar/gkp318 · 2009 · External reference
10.1093/nar/gkw357
10.1093/nar/gkw357 · External reference
ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation
10.1080/19420862.2016.1205773 · 2016 · External reference
10.1016/j.jmb.2016.08.019
10.1016/j.jmb.2016.08.019 · External reference
How can we discover developable antibody-based biotherapeutics?
10.3389/fmolb.2023.1221626 · 2023 · External reference
Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies
10.1080/19420862.2021.2008790 · 2022 · External reference
Using machine learning to predict the effects and consequences of mutations in proteins
2023 · External reference
Recent advances in machine learning variant effect prediction tools for protein engineering
10.1021/acs.iecr.1c04943 · 2022 · External reference
ProteinBERT: a universal deep-learning model of protein sequence and function
10.1093/bioinformatics/btac020 · 2022 · External reference
AbLang: an antibody language model for completing antibody sequences
10.1093/bioadv/vbac046 · 2022 · External reference
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Deciphering the language of antibodies using self-supervised learning
10.1016/j.patter.2022.100513 · 2022 · External reference
10.1101/2023.01.19.524683
10.1101/2023.01.19.524683 · External reference
BERT2DAb: a pre-trained model for antibody representation based on amino acid sequences and 2D-structure
2023 · External reference
De novo generation of antibody CDRH3 with a pre-trained generative large language model
2023 · External reference
10.1016/j.neucom.2023.127063
10.1016/j.neucom.2023.127063 · External reference
A dataset comprised of binding interactions for 104,972 antibodies against a SARS-CoV-2 peptide
10.1038/s41597-022-01779-4 · 2022 · External reference
10.1101/2024.08.06.606780
10.1101/2024.08.06.606780 · External reference
10.1016/j.csbj.2023.11.041 · Admitted local publication
10.1101/2020.04.12.024844
10.1101/2020.04.12.024844 · External reference
AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study
10.3389/fmolb.2023.1249247 · 2023 · External reference
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10.1101/2022.08.16.504181
10.1101/2022.08.16.504181 · External reference
Machine learning optimization of candidate antibody yields highly diverse sub-nanomolar affinity antibody libraries
10.1038/s41467-023-39022-2 · 2023 · External reference
10.4049/jimmunol.1601137
10.4049/jimmunol.1601137 · External reference
Antibody structure prediction using interpretable deep learning
10.1016/j.patter.2021.100406 · 2022 · External reference
10.1093/bioinformatics/btac016
10.1093/bioinformatics/btac016 · External reference
High-throughput antibody structure modeling and design using abodybuilder
10.1007/978-1-4939-8736-8_21 · 2019 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
NanoNet: Rapid and accurate end-to-end nanobody modeling by deep learning
10.3389/fimmu.2022.958584 · 2022 · External reference
10.1101/2023.08.30.555473
10.1101/2023.08.30.555473 · External reference
10.1101/2021.10.04.463034
10.1101/2021.10.04.463034 · External reference
10.1101/2023.04.26.538476
10.1101/2023.04.26.538476 · External reference
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10.1101/2024.03.14.585103
10.1101/2024.03.14.585103 · External reference
10.1101/2023.11.22.568230
10.1101/2023.11.22.568230 · External reference
Antibody-SGM: Antigen-Specific Joint Design of Antibody Sequence and Structure using Diffusion Models
2023 · External reference
10.1016/j.csbj.2022.12.021 · Admitted local publication
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RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
10.1371/journal.pcbi.1006112 · 2018 · External reference
Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening
10.1038/s41551-023-01093-3 · 2024 · External reference
Fragment-based computational design of antibodies targeting structured epitopes
10.1126/sciadv.abp9540 · 2022 · External reference
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BLAST: improvements for better sequence analysis
10.1093/nar/gkl164 · 2006 · External reference
Clustal Omega for making accurate alignments of many protein sequences
10.1002/pro.3290 · 2018 · External reference
BioPhi: A platform for antibody design, humanization, and humanness evaluation based on natural antibody repertoires and deep learning
10.1080/19420862.2021.2020203 · 2022 · External reference
The immune epitope database (IEDB): 2018 update
10.1093/nar/gky1006 · 2019 · External reference
IEDB-AR: immune epitope database—analysis resource in 2019
10.1093/nar/gkz452 · 2019 · External reference
Assessing antibody and nanobody nativeness for hit selection and humanization with AbNatiV
2024 · External reference
Humanization of antibodies using a machine learning approach on large-scale repertoire data
10.1093/bioinformatics/btab434 · 2021 · External reference
SOLart: a structure-based method to predict protein solubility and aggregation
10.1093/bioinformatics/btz773 · 2020 · External reference
Protein–Sol: a web tool for predicting protein solubility from sequence
10.1093/bioinformatics/btx345 · 2017 · External reference
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation
10.1093/nar/gkae382 · 2024 · External reference
10.1093/protein/gzw019
10.1093/protein/gzw019 · External reference
Sequence-based prediction of pH-dependent protein solubility using CamSol
10.1093/bib/bbad004 · 2023 · External reference
Boosting the full potential of PyMOL with structural biology plugins
10.3390/biom12121764 · 2022 · External reference
10.1101/2024.04.03.587755
10.1101/2024.04.03.587755 · External reference
10.1016/j.softx.2015.06.001 · Admitted local publication
Scalable molecular dynamics on CPU and GPU architectures with NAMD
10.1063/5.0014475 · 2020 · External reference
LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
10.1016/j.cpc.2021.108171 · 2022 · External reference
JPred: a consensus secondary structure prediction server
10.1093/bioinformatics/14.10.892 · 1998 · External reference
The PSIPRED protein analysis workbench: 20 years on
2019 · External reference
PredictProtein-predicting protein structure and function for 29 years
2021 · External reference
JPred4: a protein secondary structure prediction server
2015 · External reference
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function
10.1093/bioinformatics/btab762 · 2022 · External reference
10.1016/j.str.2021.01.005
10.1016/j.str.2021.01.005 · External reference
10.1021/acs.jcim.2c01083
10.1021/acs.jcim.2c01083 · External reference
10.1016/j.csbj.2020.02.021
10.1016/j.csbj.2020.02.021 · External reference
10.1016/j.csbj.2018.01.002 · Admitted local publication
Surface plasmon resonance for therapeutic antibody characterization
10.1007/978-1-4939-2617-6_3 · 2015 · External reference
10.1038/s41596-021-00536-y
10.1038/s41596-021-00536-y · External reference
Homogeneous surrogate virus neutralization assay to rapidly assess neutralization activity of anti-SARS-CoV-2 antibodies
10.1038/s41467-022-31300-9 · 2022 · External reference
Designing binding kinetic assay on the bio-layer interferometry (BLI) biosensor to characterize antibody-antigen interactions
10.1016/j.ab.2017.08.002 · 2017 · External reference
A short history, principles, and types of ELISA, and our laboratory experience with peptide/protein analyses using ELISA
10.1016/j.peptides.2015.04.012 · 2015 · External reference
Potential applications of fluorescence-activated cell sorting (facs) and droplet-based microfluidics in promoting the discovery of specific antibodies for characterizations of fish immune cells
2021 · External reference
An alternative assay to hydrophobic interaction chromatography for high-throughput characterization of monoclonal antibodies
10.1080/19420862.2015.1016694 · 2015 · External reference
High-throughput screening for developability during early-stage antibody discovery using self-interaction nanoparticle spectroscopy
10.4161/mabs.27431 · 2014 · External reference
Characterization of therapeutic mAb charge heterogeneity by iCIEF coupled to mass spectrometry (iCIEF–MS)
10.1002/elps.202200170 · 2023 · External reference
Separation of mAbs molecular variants by analytical hydrophobic interaction chromatography HPLC: overview and applications
10.4161/mabs.28693 · 2014 · External reference
A review on bioanalytical method development and validation by RP-HPLC
2014 · External reference
The Therapeutic Antibody Profiler for Computational Developability Assessment
10.1007/978-1-0716-1450-1_5 · 2022 · External reference
Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling
10.1038/s42003-023-05744-8 · 2024 · External reference
Automated optimisation of solubility and conformational stability of antibodies and proteins
10.1038/s41467-023-37668-6 · 2023 · External reference
10.1101/cshperspect.a033845
10.1101/cshperspect.a033845 · External reference
EpitopeVec: linear epitope prediction using deep protein sequence embeddings
10.1093/bioinformatics/btab467 · 2021 · External reference
EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression
10.1186/s12859-014-0414-y · 2014 · External reference
SEMA: Antigen B-cell conformational epitope prediction using deep transfer learning
10.3389/fimmu.2022.960985 · 2022 · External reference
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes
10.1093/bioinformatics/btab321 · 2021 · External reference
Conformational B-cell epitope prediction method based on antigen preprocessing and mimotopes analysis
2015 · External reference
Antibody-antigen docking and design via hierarchical structure refinement
2022 · External reference
10.1101/2024.01.13.575504
10.1101/2024.01.13.575504 · External reference
ProtGPT2 is a deep unsupervised language model for protein design
10.1038/s41467-022-32007-7 · 2022 · External reference
10.1016/j.cels.2023.10.002
10.1016/j.cels.2023.10.002 · External reference
Reprogramming Pretrained Language Models for Antibody Sequence Infilling
2023 · External reference
Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB. 1.5 spike protein
10.1038/s41467-024-46104-2 · 2024 · External reference
Predicting antibody affinity changes upon mutations by combining multiple predictors
10.1038/s41598-020-76369-8 · 2020 · External reference
10.1002/pro.2829
10.1002/pro.2829 · External reference
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures
10.1093/nar/gkw458 · 2016 · External reference
10.1038/nm.3743
10.1038/nm.3743 · External reference
BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data
10.1186/s13073-018-0528-3 · 2018 · External reference
10.1371/journal.pcbi.1012646
10.1371/journal.pcbi.1012646 · External reference
Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features
10.1080/19420862.2022.2163584 · 2023 · External reference
10.1101/2023.12.08.570889
10.1101/2023.12.08.570889 · External reference
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10.1101/2023.11.06.565922
10.1101/2023.11.06.565922 · External reference
10.1101/2023.12.19.572475
10.1101/2023.12.19.572475 · External reference
10.1093/bioadv/vbae202
10.1093/bioadv/vbae202 · External reference
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10.1038/s41587-023-01763-2
10.1038/s41587-023-01763-2 · External reference
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