ArticleBMC bioinformatics2013
ClusCo: clustering and comparison of protein models.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Importance of Secondary Structure Data in Large Scale Protein Modeling Using Low-Resolution SURPASS Method.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Clues to the Design of Aggregation-Resistant Insulin from Proline Scanning of Highly Amyloidogenic Peptides Derived from the N-Terminal Segment of the A-Chain.Molecular pharmaceutics · 2024Article
- Towards discovery of inhibitors of the undecaprenyl-pyrophosphate phosphatase BacA by virtual high-throughput screening.Computational and structural biotechnology journal · 2022Article
- Potential Novel Thioether-Amide or Guanidine-Linker Class of SARS-CoV-2 Virus RNA-Dependent RNA Polymerase Inhibitors Identified by High-Throughput Virtual Screening Coupled to Free-Energy Calculations.International journal of molecular sciences · 2021Article
- Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLMolecules (Basel, Switzerland) · 2020Article
- Ranking near-native candidate protein structures via random forest classification.BMC bioinformatics · 2019Article
- Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFκB promoter.Nucleic acids research · 2019Article
- Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis.Frontiers in microbiology · 2018Article
- Identify High-Quality Protein Structural Models by EnhancedBioMed research international · 2017Article
- UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data.BMC bioinformatics · 2016Article
- fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.Bioinformatics (Oxford, England) · 2014Article
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
- Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.Journal of molecular modeling · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline.
resultsClusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering.
conclusionsThe application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU, which resulted in a significant speedup over similar clustering and scoring computation programs.
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