ArticleProteins2018
Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.
Article in Proteins, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A Computational Approach for the Prediction of p53 and BCL-2 Protein-Protein Interactions.International journal of molecular sciences · 2025Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Assembly of Protein Complexes In and On the Membrane with Predicted Spatial Arrangement Constraints.bioRxiv : the preprint server for biology · 2023Article
- Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD.Proteomics · 2023Article
- Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- LZerD Protein-Protein Docking Webserver Enhanced WithFrontiers in molecular biosciences · 2021Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Performance and Its Limits in Rigid Body Protein-Protein Docking.Structure (London, England : 1993) · 2020Article
- Article
- ClusPro LigTBM: Automated Template-based Small Molecule Docking.Journal of molecular biology · 2020Article
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- SWISS-MODEL: homology modelling of protein structures and complexes.Nucleic acids research · 2018Article
- Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures.International journal of molecular sciences · 2017Review
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4 authors.
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Abstract
We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZerD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase.
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