AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Design
Fuente:
arXiv
Saved in:
| Main Authors: | Zhao, Xinyan, Tang, Yi-Ching, Singh, Akshita, Cantu, Victor J, An, KwanHo, Lee, Junseok, Stogsdill, Adam E, Hamdi, Ibraheem M, Ramesh, Ashwin Kumar, An, Zhiqiang, Jiang, Xiaoqian, Kim, Yejin |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Structure-Aware Antibody Design with Affinity-Optimized Inverse Folding
by: Zhao, Xinyan, et al.
Published: (2025)
by: Zhao, Xinyan, et al.
Published: (2025)
From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning
by: Min, Yaosen, et al.
Published: (2022)
by: Min, Yaosen, et al.
Published: (2022)
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction
by: Schapin, Nikolai, et al.
Published: (2024)
by: Schapin, Nikolai, et al.
Published: (2024)
Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
by: Baillif, Benoit, et al.
Published: (2024)
by: Baillif, Benoit, et al.
Published: (2024)
Investigating Knowledge Distillation Through Neural Networks for Protein Binding Affinity Prediction
by: Abbasi, Wajid Arshad, et al.
Published: (2026)
by: Abbasi, Wajid Arshad, et al.
Published: (2026)
Improving Antibody Design with Force-Guided Sampling in Diffusion Models
by: Kulytė, Paulina, et al.
Published: (2024)
by: Kulytė, Paulina, et al.
Published: (2024)
Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Design
by: Crouzet, Simon J.
Published: (2026)
by: Crouzet, Simon J.
Published: (2026)
Interpretable Multimodal Learning for Tumor Protein-Metal Binding: Progress, Challenges, and Perspectives
by: Liu, Xiaokun, et al.
Published: (2025)
by: Liu, Xiaokun, et al.
Published: (2025)
ImmunoAI: Accelerated Antibody Discovery Using Gradient-Boosted Machine Learning with Thermodynamic-Hydrodynamic Descriptors and 3D Geometric Interface Topology
by: Shivakumar, Shawnak, et al.
Published: (2025)
by: Shivakumar, Shawnak, et al.
Published: (2025)
Computational predictions of nutrient precipitation for intensified cell 1 culture media via amino acid solution thermodynamics
by: Reddy, Jayanth Venkatarama, et al.
Published: (2025)
by: Reddy, Jayanth Venkatarama, et al.
Published: (2025)
Protein folding classes -- High-dimensional geometry of amino acid composition space revisited
by: Mao, Boryeu
Published: (2025)
by: Mao, Boryeu
Published: (2025)
GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
by: Lindsey, Michael
Published: (2026)
by: Lindsey, Michael
Published: (2026)
Explainable Machine Learning and Deep Learning Models for Predicting TAS2R-Bitter Molecule Interactions
by: Ferri, Francesco, et al.
Published: (2024)
by: Ferri, Francesco, et al.
Published: (2024)
Canonicalization of the E value from BLAST similarity search -- dissimilarity measure and distance function for a metric space of protein sequences
by: Mao, Boryeu
Published: (2025)
by: Mao, Boryeu
Published: (2025)
Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
by: Reilly, Charles B
Published: (2026)
by: Reilly, Charles B
Published: (2026)
AntiFold: Improved antibody structure-based design using inverse folding
by: Høie, Magnus Haraldson, et al.
Published: (2024)
by: Høie, Magnus Haraldson, et al.
Published: (2024)
HelixVS: Deep Learning-Enhanced Structure-Based Platform for Screening and Design
by: Zhang, Shanzhuo, et al.
Published: (2025)
by: Zhang, Shanzhuo, et al.
Published: (2025)
EscalNet: Learn isotropic representation space for biomolecular dynamics based on effective energy
by: Zuo, Guanghong
Published: (2025)
by: Zuo, Guanghong
Published: (2025)
Network Pharmacology Framework Characterizes Polypharmacological Properties of Dietary Flavonoids: Integration of Computational, Experimental, and Epidemiological Evidence
by: Fujisaki, Koyo, et al.
Published: (2026)
by: Fujisaki, Koyo, et al.
Published: (2026)
Persistent Sheaf Laplacian Analysis of Protein Flexibility
by: Hayes, Nicole, et al.
Published: (2025)
by: Hayes, Nicole, et al.
Published: (2025)
Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases
by: Di Gregorio, Elisabetta, et al.
Published: (2023)
by: Di Gregorio, Elisabetta, et al.
Published: (2023)
mRNA Folding Algorithms for Structure and Codon Optimization
by: Ward, Max, et al.
Published: (2025)
by: Ward, Max, et al.
Published: (2025)
Two for the Price of One: Integrating Large Language Models to Learn Biophysical Interactions
by: Clark, Joseph D., et al.
Published: (2025)
by: Clark, Joseph D., et al.
Published: (2025)
Quantifying the uncertainty of molecular dynamics simulations : Good-Turing statistics revisited
by: Tsampazi, Vasiliki, et al.
Published: (2026)
by: Tsampazi, Vasiliki, et al.
Published: (2026)
Predicting Protein-Nucleic Acid Flexibility Using Persistent Sheaf Laplacians
by: Hayes, Nicole, et al.
Published: (2025)
by: Hayes, Nicole, et al.
Published: (2025)
Quantification of protein homodimer affinity using native mass spectrometry
by: Schulte, Jonathan, et al.
Published: (2025)
by: Schulte, Jonathan, et al.
Published: (2025)
Conformational landscapes in cryo-ET data based on MD simulations
by: Jonic, Slavica
Published: (2026)
by: Jonic, Slavica
Published: (2026)
Combining oligo pools and Golden Gate cloning to create protein variant libraries or guide RNA libraries for CRISPR applications
by: Valero, Alicia Maciá, et al.
Published: (2024)
by: Valero, Alicia Maciá, et al.
Published: (2024)
Non-perturbative Bacterial Identification Directly from Solid Agar Plates Using Raman
by: Kim, Jeong Hee, et al.
Published: (2026)
by: Kim, Jeong Hee, et al.
Published: (2026)
VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels
by: Wang, Rui, et al.
Published: (2026)
by: Wang, Rui, et al.
Published: (2026)
Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning
by: Clark, Joseph D., et al.
Published: (2024)
by: Clark, Joseph D., et al.
Published: (2024)
Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
by: Lim, Hocheol, et al.
Published: (2025)
by: Lim, Hocheol, et al.
Published: (2025)
Impact of Force Field Polarization on Correlated Motions of Proteins
by: Milinski, Ana, et al.
Published: (2025)
by: Milinski, Ana, et al.
Published: (2025)
Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
by: Ghafouri, Hamidreza, et al.
Published: (2025)
by: Ghafouri, Hamidreza, et al.
Published: (2025)
LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models
by: Phan, An, et al.
Published: (2026)
by: Phan, An, et al.
Published: (2026)
Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold
by: Chib, Garima, et al.
Published: (2025)
by: Chib, Garima, et al.
Published: (2025)
Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction
by: Yin, Song, et al.
Published: (2023)
by: Yin, Song, et al.
Published: (2023)
Marginal Girsanov Reweighting: Stable Variance Reduction for Long-Timescale Dynamics from Biased Simulation
by: Wang, Yan, et al.
Published: (2025)
by: Wang, Yan, et al.
Published: (2025)
Benchmarking open-source tools for in silico antiviral drug discovery
by: Elton, Daniel C., et al.
Published: (2026)
by: Elton, Daniel C., et al.
Published: (2026)
Co-Evolution-Based Metal-Binding Residue Prediction with Graph Neural Networks
by: Rastegari, Sayedmohammadreza, et al.
Published: (2025)
by: Rastegari, Sayedmohammadreza, et al.
Published: (2025)
Similar Items
-
Structure-Aware Antibody Design with Affinity-Optimized Inverse Folding
by: Zhao, Xinyan, et al.
Published: (2025) -
From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning
by: Min, Yaosen, et al.
Published: (2022) -
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction
by: Schapin, Nikolai, et al.
Published: (2024) -
Benchmarking structure-based three-dimensional molecular generative models using GenBench3D: ligand conformation quality matters
by: Baillif, Benoit, et al.
Published: (2024) -
Investigating Knowledge Distillation Through Neural Networks for Protein Binding Affinity Prediction
by: Abbasi, Wajid Arshad, et al.
Published: (2026)