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ClusCo: clustering and comparison of protein models
[article]
2013
arXiv
pre-print
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Results: Clusco 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 ...
The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. ...
Background The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. ...
arXiv:1302.4000v1
fatcat:vxykaaxx3jdbfjoq7al6pteume
UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data
2016
BMC Bioinformatics
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In addition to ranking and clustering of large sets of models of the same protein or RNA molecule, uQlust can also be used in conjunction with fragment-based profiles in order to cluster structures of ...
a linear-time algorithm for implicit comparison of all pairs of models with profile hashing to enable efficient clustering of large data sets with a low memory footprint. ...
Mahendra Thapa's help with generating structure sets used for benchmarking, and Mr. Prakash Velayutham's technical help. ...
doi:10.1186/s12859-016-1381-2
pmid:28031034
pmcid:PMC5198500
fatcat:vwhs3msgd5g2peyvqci5pyedxy
Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis
2019
Frontiers in Microbiology
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A pharmacophore model was designed on a known bisphosphonate BPH-629 and used to prepare an enriched compound library that was further docked into UppS conformational ensemble generated by molecular dynamics ...
We report the successful implementation of virtual screening in the discovery of new inhibitors of undecaprenyl pyrophosphate synthase (UppS) from Escherichia coli. ...
MD snapshots in 100 ps increments were collected (200 protein conformation models), clustered using ClusCo software and visually analyzed with Pymol 3 software (DeLano, 2002) . ...
doi:10.3389/fmicb.2018.03322
pmid:30692977
pmcid:PMC6339874
fatcat:sub2ydlvxfe7lldv7yo45ribda
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
2021
International Journal of Molecular Sciences
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This viral protein is without a human counterpart and thus represents a unique prospective drug target. ...
available as well as suitable for further biological evaluation and mode of action studies. ...
We thank OpenEye for the academic licensing of their software and their help and support. We thank Elmar Krieger for his support and help. ...
doi:10.3390/ijms222011143
pmid:34681802
fatcat:wubouw6uefcqxgkr6kg4fhtkia
Identify High-Quality Protein Structural Models by EnhancedK-Means
2017
BioMed Research International
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when the decoy population increases.Results.Here, we proposed two enhancedK-means clustering algorithms capable of robustly identifying high-quality protein structural models. ...
Background.One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated ...
Acknowledgments This paper is supported by Grants nos. 61540058 and 61202290 under the National Natural Science Foundation of China (http://www.nsfc.gov.cn). ...
doi:10.1155/2017/7294519
pmid:28421198
pmcid:PMC5381204
fatcat:eyvtbb5dezbktleykrnb574ft4
Ranking near-native candidate protein structures via random forest classification
2019
BMC Bioinformatics
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The clustered central structures with the most number of neighbors are frequently regarded as the near-native protein structures with the lowest free energy; however, limitations in clustering methods ...
The results confirmed that the identification of the first model were closer to the native structure in 12 of 43 cases versus four for SPICKER, and the same as the native structure in up to 27 of 43 cases ...
Acknowledgments The authors acknowledge and thank the anonymous reviewers for their suggestions that allowed the improvement of our manuscript. ...
doi:10.1186/s12859-019-3257-8
pmid:31874596
pmcid:PMC6929337
fatcat:jdbwqkz7oba33mhka2wmpipb2a
Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors
2014
Biophysical Journal
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The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. ...
The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. ...
Structural clustering was performed with the K-means algorithm (using ClusCo software (47) ). ...
doi:10.1016/j.bpj.2014.04.022
pmid:24896119
pmcid:PMC4052351
fatcat:offixx3kcfdxda63e53z747sre
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model
[chapter]
2016
Msphere
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This chapter also presents CABS-based modeling methods, including multiscale tools for de novo structure prediction, modeling of protein dynamics and prediction of protein-peptide complexes. ...
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the ...
Acknowledgments Funding for this work was supported by the National Science Center grant [MAESTRO 2014/14/A/ST6/0008] and by the Foundation for Polish Science TEAM project (TEAM/2011-7/6) co-financed by ...
doi:10.1007/978-1-4939-6406-2_8
pmid:27787822
fatcat:tufskifl6jdwrblj5hgg6caoya
Structural variation of protein-ligand complexes of the first bromodomain of BRD4
2021
Organic and biomolecular chemistry
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The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. ...
Notes and references ...
H. is supported by the Royal Academy of Engineering under the Chairs in Emerging Technologies scheme. ...
doi:10.1039/d1ob00658d
pmid:34105560
fatcat:7rzgvh6hifenll5hdrxrxtfbd4
COARSE-GRAINED MODELING OF PROTEIN STRUCTURE, DYNAMICS AND PROTEIN-PROTEIN INTERACTIONS
2014
TASK Quarterly
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We developed and validated a novel multiscale methodology for the study of protein folding processes including flexible docking of proteins and peptides. ...
This paper focuses on the description of the coarse-grained CABS model and its selected applications. ...
DEC-2011/01/D/NZ2/07683, and from Polish Ministry of Science and Higher Education, Grant No. IP2012 016872. ...
doi:10.17466/tq2014/18.3/b
doaj:ff0e72eee8f94cf39d9df15ed6c6a9de
fatcat:r7465ibcina6tfy4dqd5q7adwm
Phosphorylation orchestrates the structural ensemble of the intrinsically disordered protein HMGA1a and modulates its DNA binding to the NFκB promoter
2019
Nucleic Acids Research
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High Mobility Group Protein A1a (HMGA1a) is a highly abundant nuclear protein, which plays a crucial role during embryogenesis, cell differentiation, and neoplasia. ...
The CK2-, cdc2- and cdc2/CK2-phosphorylated forms of HMGA1a each exhibit a different binding affinity towards the PRD2 element of the NFκB promoter. ...
The independent ensembles were grouped into eight structural clusters by an RMSDbased clustering method using the Clusco software package (12, 57) . ...
doi:10.1093/nar/gkz614
pmid:31340016
pmcid:PMC7145567
fatcat:2ou47utqnnen5khz2u3dlxikxy
Protein structure refinement using a quantum mechanics-based chemical shielding predictor
2017
Chemical Science
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We show that a QM-based predictor of a protein backbone and CB chemical shifts is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes ...
clustering. ...
The values in parenthesis are the CA RMSD deviations of the ProCS15 annealed ensemble structure relative to the ensemble cluster centroid that served as a starting point for the annealing Protein
Annealed ...
doi:10.1039/c6sc04344e
pmid:28451325
pmcid:PMC5399634
fatcat:gwntcexnj5g5re6aigbuyrgcge
Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA
2014
Journal of Molecular Modeling
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This algorithm is based on the twophase alignment of protein structures when matching fragments of the compared proteins. ...
Searching for similar 3D protein structures is one of the primary processes employed in the field of structural bioinformatics. ...
[19] , CASSERT [13] , ClusCo [20] , and others [21, 22] . ...
doi:10.1007/s00894-014-2067-1
pmid:24481593
pmcid:PMC3936136
fatcat:aivfhc5u6jgezpi2nylwnuru4u