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Updated: Aug 15, 2026

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
Docking to single-domain and multiple-domain proteins: old and new challenges
E Ben-Zeev1, N Kowalsman, A Ben-Shimon
1Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.
The MolFit program shows high sensitivity for protein-ligand docking, accurately predicting structures with minor changes. However, its selectivity needs improvement for NMR or modeled structures and complex scenarios involving domain movements.
Area of Science:
- Computational Biology
- Structural Bioinformatics
- Molecular Docking
Background:
- The Critical Assessment of PRedicted Interactions (CAPRI) experiments evaluate protein-ligand docking programs.
- Rigid-body docking programs like MolFit are essential tools for predicting complex structures.
- Existing docking programs face challenges with conformational changes and lack of external data.
Purpose of the Study:
- To assess the performance and limitations of the rigid-body docking program MolFit.
- To identify areas for improvement in MolFit's sensitivity and selectivity.
- To explore methods for handling large conformational changes in docking.
Main Methods:
- Utilized a diverse set of targets from CAPRI experiments to test MolFit.
- Employed rigid multibody multistage docking procedures to accommodate domain movements.
- Analyzed MolFit's performance with moderate local and large global conformational changes.
Main Results:
- MolFit demonstrated high sensitivity, producing accurate docking solutions for structures with moderate local changes.
- The program's selectivity requires readjustment for NMR or modeled structures and when external data is unavailable.
- Rigid multibody multistage docking effectively handled large global conformational changes within the rigid-body approximation.
Conclusions:
- MolFit is a sensitive tool for rigid-body docking but needs enhanced selectivity for challenging cases.
- Multistage docking strategies are effective for accommodating significant domain movements.
- Further development is needed to improve ranking of docking solutions, especially in data-scarce scenarios.
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