Search Results - "Gront D"

Exploring P450 superfamily diversity with P450Atlas - Online tool for automated subfamily assignment.

Authors: Gront D Syed K Nelson DR

Source: Protein science : a publication of the Protein Society [Protein Sci] 2025 Mar; Vol. 34 (3), pp. e70057.

Publication Type: Journal Article

Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

deepBBQ: A Deep Learning Approach to the Protein Backbone Reconstruction.

Authors: Kryś JD Głowacki M Śmieja P et al.

Source: Biomolecules [Biomolecules] 2024 Nov 14; Vol. 14 (11). Date of Electronic Publication: 2024 Nov 14.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.

Authors: Koehler Leman J Lyskov S Lewis SM et al.

Source: Nature communications [Nat Commun] 2021 Nov 29; Vol. 12 (1), pp. 6947. Date of Electronic Publication: 2021 Nov 29.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

VisuaLife: library for interactive visualization in rich web applications.

Authors: Kryś JD Gront D

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2021 Oct 25; Vol. 37 (20), pp. 3662-3663.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE; PubMed not MEDLINE

In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria.

Authors: Msomi NN Padayachee T Nzuza N et al.

Source: Molecules (Basel, Switzerland) [Molecules] 2021 Mar 11; Vol. 26 (6). Date of Electronic Publication: 2021 Mar 11.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049 (Electronic) Linking ISSN: 14203049 NLM ISO Abbreviation: Molecules Subsets: MEDLINE

Coarse-grained potential for hydrogen bond interactions.

Authors: Kryś JD Gront D

Source: Journal of molecular graphics & modelling [J Mol Graph Model] 2023 Nov; Vol. 124, pp. 108507. Date of Electronic Publication: 2023 May 23.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Elsevier Science, Inc Country of Publication: United States NLM ID: 9716237 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-4243 (Electronic) Linking ISSN: 10933263 NLM ISO Abbreviation: J Mol Graph Model Subsets: MEDLINE

Better together: Elements of successful scientific software development in a distributed collaborative community.

Authors: Koehler Leman J Weitzner BD Renfrew PD et al.

Corporate Authors: Koehler Leman J Weitzner BD Renfrew PD et al.

Source: PLoS computational biology [PLoS Comput Biol] 2020 May 04; Vol. 16 (5), pp. e1007507. Date of Electronic Publication: 2020 May 04 (Print Publication: 2020).

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Review

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks.

Authors: Saqib MN Kryś JD Gront D

Source: Biomolecules [Biomolecules] 2022 Jun 17; Vol. 12 (6). Date of Electronic Publication: 2022 Jun 17.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101596414 Publication Model: Electronic Cited Medium: Internet ISSN: 2218-273X (Electronic) Linking ISSN: 2218273X NLM ISO Abbreviation: Biomolecules Subsets: MEDLINE

Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria.

Authors: Msweli S Chonco A Msweli L et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2022 May 22; Vol. 23 (10). Date of Electronic Publication: 2022 May 22.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters.

Authors: Nkosi BVZ Padayachee T Gront D et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2022 May 02; Vol. 23 (9). Date of Electronic Publication: 2022 May 02.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species.

Authors: Malinga NA Nzuza N Padayachee T et al.

Source: Microorganisms [Microorganisms] 2022 Apr 21; Vol. 10 (5). Date of Electronic Publication: 2022 Apr 21.

Publication Type: Journal Article

Journal Info: Publisher: MDPI AG Country of Publication: Switzerland NLM ID: 101625893 Publication Model: Electronic Cited Medium: Print ISSN: 2076-2607 (Print) Linking ISSN: 20762607 NLM ISO Abbreviation: Microorganisms Subsets: PubMed not MEDLINE

Diversification of Ferredoxins across Living Organisms.

Authors: Nzuza N Padayachee T Chen W et al.

Source: Current issues in molecular biology [Curr Issues Mol Biol] 2021 Sep 30; Vol. 43 (3), pp. 1374-1390. Date of Electronic Publication: 2021 Sep 30.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 100931761 Publication Model: Electronic Cited Medium: Internet ISSN: 1467-3045 (Electronic) Linking ISSN: 14673037 NLM ISO Abbreviation: Curr Issues Mol Biol Subsets: MEDLINE

In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles.

Authors: Akapo OO Macnar JM Kryś JD et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2021 Jul 22; Vol. 22 (15). Date of Electronic Publication: 2021 Jul 22.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species.

Authors: Nzuza N Padayachee T Syed PR et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2021 May 24; Vol. 22 (11). Date of Electronic Publication: 2021 May 24.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

BioShell-Threading: versatile Monte Carlo package for protein 3D threading.

Authors: Gniewek P Kolinski A Kloczkowski A et al.

Source: BMC bioinformatics [BMC Bioinformatics] 2014 Jan 20; Vol. 15, pp. 22. Date of Electronic Publication: 2014 Jan 20.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE

Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures.

Authors: Gront D Grabowski M Zimmerman MD et al.

Source: Journal of structural and functional genomics [J Struct Funct Genomics] 2012 Dec; Vol. 13 (4), pp. 213-25. Date of Electronic Publication: 2012 Oct 20.

Publication Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: Kluwer Academic Publishers Country of Publication: Netherlands NLM ID: 101128185 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1570-0267 (Electronic) Linking ISSN: 1345711X NLM ISO Abbreviation: J Struct Funct Genomics Subsets: MEDLINE

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.

Authors: Gront D Blaszczyk M Wojciechowski P et al.

Source: Nucleic acids research [Nucleic Acids Res] 2012 Jul; Vol. 40 (Web Server issue), pp. W257-62. Date of Electronic Publication: 2012 Jun 12.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Generalized fragment picking in Rosetta: design, protocols and applications.

Authors: Gront D Kulp DW Vernon RM et al.

Source: PloS one [PLoS One] 2011; Vol. 6 (8), pp. e23294. Date of Electronic Publication: 2011 Aug 24.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium.

Authors: Mnguni FC Padayachee T Chen W et al.

Source: International journal of molecular sciences [Int J Mol Sci] 2020 Jul 07; Vol. 21 (13). Date of Electronic Publication: 2020 Jul 07.

Publication Type: Journal Article

Journal Info: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Authors: Leman JK Weitzner BD Lewis SM et al.

Source: Nature methods [Nat Methods] 2020 Jul; Vol. 17 (7), pp. 665-680. Date of Electronic Publication: 2020 Jun 01.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE