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Analysis of internal residue-residue interactions within antibodies
NEW
Prediction of 3D structures from antibody sequences, followed by analysis of the types and distances of internal residue-residue interactions
Application Scenarios
Investigation of antibody structural stability, heavy-light chain pairing mechanisms, and guidance for mutagenesis design.
Task Objectives
Addressing the challenge of determining spatial relationships between residues when only sequence information is available, enabling rapid identification of key interaction sites that affect folding, stability, and affinity.
Workflow
1
Antibody structure prediction
Tool：
Input：
Amino acid sequences of the variable regions of the heavy and light chains (for conventional antibodies) or the heavy chain sequence alone (for nanobodies)
Output：
Predicted PDB structure file
Explanation：
Utilizes the ImmuneBuilder model, optimized based on AlphaFold-Multimer, to rapidly generate high-accuracy 3D antibody conformations, supporting both conventional antibodies and nanobodies.
2
Residue interaction calculation
Tool：
Input：
PDB file generated in the previous step + target chain(s) (e.g., heavy/light chain) + interaction type (optional).
Output：
Table of residue interaction pairs, including chain identifiers, residue numbers, distances, and interaction types.
Explanation：
Automatically identifies intra-chain and inter-chain interactions of various types (e.g., hydrophobic, hydrogen bonds, aromatic, disulfide bonds, etc.), with support for interactive filtering (e.g., displaying only heavy–light chain interactions).
RCSB target search and de novo antibody design
NEW
Starting from known antigen–antibody complex structures, identify functional epitopes and design novel binding antibodies
Application Scenarios
Develop entirely new therapeutic antibodies against known targets, circumventing patented sequences.
Task Objectives
Enable structure-based de novo design of high-affinity therapeutic antibodies with novel CDR sequences—without requiring pre-existing antibody sequences—by leveraging publicly available structural data.
Workflow
1
Query target structure
Tool：
Input：
Target keyword(s) (e.g., “PD-L1 PD-1”).
Output：
Antigen–antibody (or receptor) complex PDB file (e.g., 3BIK).
Explanation：
Download the complex structure of the target antigen bound to a natural antibody or receptor from public structural databases (e.g., RCSB PDB).
2
Identification of functional epitopes
Tool：
Input：
Complex PDB file + antigen chain and receptor chain (e.g., Chain A and Chain B).
Output：
List of hotspot residues on the antigen involved in binding (e.g., A18, A54, A115, etc.).
Explanation：
Functional epitope residues on the antigen are extracted by analyzing the antigen–receptor interface interactions, serving as design targets for subsequent antibody engineering.
3
Design of novel antibodies
Tool：
Input：
Target antigen PDB + template antibody PDB (e.g., a human antibody from SAbDab such as 9HXO) + hotspot residues + CDR design parameters.
Output：
Multiple newly designed antibody–antigen complex structures and corresponding sequences.
Explanation：
Leverages an integrated pipeline of RFdiffusion, RoseTTAFold2, and ProteinMPNN to de novo generate high-affinity antibody CDR loops tailored to the specified epitope.
AbMart Hot Target Query and Antibody Design
NEW
Rapidly retrieve target structures from the AbSeek internal database and initiate the antibody design workflow
Application Scenarios
Develop entirely novel antibodies against high-priority or popular therapeutic targets.
Task Objectives
Addresses the fragmentation between target identification and antibody design by integrating target background information, structural data, and design capabilities into a unified, streamlined platform—significantly reducing early-stage R&D cycle time.
Workflow
1
Query target structure
Tool：
Input：
Search by target name or disease-related keywords.
Output：
Obtain target structures pre-curated by our team via “AbSeek – Target Structure and Antibody Development – Antibody Design”.tibody Design”
Explanation：
Retrieve well-annotated, popular target structures from the AbSeek proprietary database to instantly inspect structural features—saving time on manual structure searches. Users can also access target-related information in AbMart, including R&D pipeline status, gene details, and mutation sites.
2
Design novel antibodies
Tool：
Input：
Automatically populated target PDB from the previous step + user-provided template antibody + manually selected hotspot residues.
Output：
Multiple newly designed antibody–antigen complex structures and corresponding sequences.
Explanation：
Seamlessly integrates target structure retrieval with antibody generation in a single workflow, minimizing manual file downloads and uploads.
