ArticleProteins2012
Multi-LZerD: multiple protein docking for asymmetric complexes.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 95 citations in OpenAlex.
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- Precise targeting of transcriptional co-activators YAP/TAZ annihilates chemoresistant brCSCs by alteration of their mitochondrial homeostasis.Signal transduction and targeted therapy · 2025Article
- Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure.Interdisciplinary sciences, computational life sciences · 2024Review
- CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2.Nature methods · 2024Article
- Flexible protein-protein docking with a multitrack iterative transformer.Protein science : a publication of the Protein Society · 2024Article
- Sampling and Scoring in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study.Proteomics · 2023Article
- Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.Bioinformatics (Oxford, England) · 2023Article
- Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2.bioRxiv : the preprint server for biology · 2023Article
- Pairwise and Multi-chain Protein Docking Enhanced Using LZerD Web Server.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Editorial: Insights in protein biochemistry: protein biophysics 2022.Frontiers in molecular biosciences · 2023Article
- Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search.Nature communications · 2022Article
- Multi-level analysis of intrinsically disordered protein docking methods.Methods (San Diego, Calif.) · 2022Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
- MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Frontiers in molecular biosciences · 2022Article
- Article
- Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom.Bio-protocol · 2021Article
- LZerD webserver for pairwise and multiple protein-protein docking.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly. However, solving protein complex structures by experimental methods is often more difficult than single protein structures. Here, we have developed a novel computational multiple protein docking algorithm, Multi-LZerD, that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins. A genetic algorithm is applied to explore the conformational space followed by a structure refinement procedure. Benchmark on eleven hetero-multimeric complexes resulted in near-native conformations for all but one of them (a root mean square deviation smaller than 2.5Å). We also show that our method copes with unbound docking cases well, outperforming the methodology that can be directly compared with our approach. Multi-LZerD was able to predict near-native structures for multimeric complexes of various topologies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.