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ClusCo: clustering and comparison of protein models [article]

Jamróz Michał, Koliński Andrzej
2013 arXiv   pre-print
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

Rafal Adamczak, Jarek Meller
2016 BMC Bioinformatics  
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

Marko Jukič, Kaja Rožman, Matej Sova, Hélène Barreteau, Stanislav Gobec
2019 Frontiers in Microbiology  
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

Marko Jukič, Dušanka Janežič, Urban Bren
2021 International Journal of Molecular Sciences  
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

Hongjie Wu, Haiou Li, Min Jiang, Cheng Chen, Qiang Lv, Chuang Wu
2017 BioMed Research International  
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

Hongjie Wu, Hongmei Huang, Weizhong Lu, Qiming Fu, Yijie Ding, Jing Qiu, Haiou Li
2019 BMC Bioinformatics  
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

Sebastian Kmiecik, Michal Jamroz, Michal Kolinski
2014 Biophysical Journal  
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]

Sebastian Kmiecik, Andrzej Kolinski
2016 Msphere  
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

Ellen Guest, Stephen Pickett, Jonathan Hirst
2021 Organic and biomolecular chemistry  
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

ANDRZEJ KOLINSKI, SEBASTIAN KMIECIK, MICHAL JAMROZ, MACIEJ BŁASZCZYK, MAKSIM KOUZA, MATEUSZ KURCINSKI
2014 TASK Quarterly  
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  
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

Lars A. Bratholm, Jan H. Jensen
2017 Chemical Science  
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

Dariusz Mrozek, Miłosz Brożek, Bożena Małysiak-Mrozek
2014 Journal of Molecular Modeling  
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