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Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

FDB&FragLinker: A Large Fragment Database for Rapid Ligand Optimization Within Protein-Ligand Complex.

Lei Zheng¹, Qisheng Zhou², Tianxiang Fu³

¹NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200124, China; Department of Chemistry, New York University, New York, NY 10003, USA.

Journal of Molecular Biology

|March 9, 2026

Summary

Fragment-based drug design is enhanced by FDB&FragLinker, a tool for exploring and reassembling molecular fragments. This covalent docking approach generates high-quality 3D ligand complexes faster than other methods.

Keywords:

fragment database ligand optimization protein–ligand complex structure generation

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Last Updated: Mar 11, 2026

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

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Published on: March 3, 2021

Area of Science:

Computational chemistry
Drug discovery
Structural biology

Background:

Fragment-based drug design is a key strategy for identifying high-quality drug leads.
Existing methods for molecular modeling and optimization have limitations in speed and structural accuracy.

Purpose of the Study:

To introduce FDB&FragLinker, an integrated database and covalent optimization tool.
To enable efficient exploration, modification, and reassembly of molecular fragments for drug design.

Main Methods:

Utilizing fragments from DrugBank and the ZINC database (800M molecules).
Implementing a novel 3D complex generation tool based on fragment-level covalent docking.
Precisely attaching fragments to small molecules at designated connection atoms.

Main Results:

Generated high-quality 3D protein-optimized ligand complex structures.
Achieved greater structural fidelity compared to traditional docking methods.
Demonstrated significantly faster performance than recent diffusion-based generative models.

Conclusions:

FDB&FragLinker offers a powerful and efficient approach for small molecule optimization and modification.
The tool is versatile, applicable to PROTACs, small molecule polypeptides, and more.
FDB&FragLinker is open-source and accessible via a web server and GitHub.