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Article ; Online: Glass reinforced plastic (GRP) boats and the impact on coastal environment - Evidence of fibreglass ingestion by marine bivalves from natural populations.

Ciocan, Corina / Annels, Claude / Fitzpatrick, Megan / Couceiro, Fay / Steyl, Ilse / Bray, Simon

2024 Volume 472, Page(s) 134619

Abstract: Classified as marine debris, man made materials are polluting the world's oceans. Recently, glass reinforced plastic (GRP) has been shown to degrade and contaminate the coasts. In this pioneering study, fibreglass particles have been detected in the soft ...

Abstract	Classified as marine debris, man made materials are polluting the world's oceans. Recently, glass reinforced plastic (GRP) has been shown to degrade and contaminate the coasts. In this pioneering study, fibreglass particles have been detected in the soft parts of oysters and mussels collected from natural populations, in front of an active boatyard. The presence of particulate glass, with concentrations up to 11,220 particles/kg ww in Ostrea edulis and 2740 particles/kg ww in Mytilus edulis, was confirmed by micro Raman spectroscopy. The results showed higher accumulation during the winter months, when boat maintenance activities are peaking and, through repair work, the release of glass fibres in the environment is more likely. Bivalves are considered high risk species due to their sessile nature and extensive filter feeding behaviour. The microparticle inclusion may contribute to adverse impacts on physiological processes and eventually to a decline in the overall health and subsequent death of the animal. The high costs involved in the proper GRP disposal and the lack of recycling facilities worldwide lead to boat abandonement and further contamination of the coasts. For the first time this study presents the extensive fibreglass contamination of natural bivalve populations, in a popular South England sailing harbour, designated a biological and geological site of specific scientific interest (SSRI).
Language	English
Publishing date	2024-05-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2024.134619
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Ligand Unbinding Pathway and Mechanism Analysis Assisted by Machine Learning and Graph Methods.

Bray, Simon / Tänzel, Victor / Wolf, Steffen

Journal of chemical information and modeling

2022 Volume 62, Issue 19, Page(s) 4591–4604

Abstract: We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for ... ...

Abstract	We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for reducing the dimensionality of the input data, followed by identification of unbinding paths and training a machine learning model for trajectory clustering. The second approach clusters trajectories according to their pairwise mean Euclidean distance employing the neighbor-net algorithm, which takes into account input data bias in the distances set and is superior to dendrogram construction. Finally, we describe a more complex case where the reaction coordinate relevant for path identification is a single intraligand hydrogen bond, highlighting the challenges involved in unbinding path reaction coordinate detection.
MeSH term(s)	Kinetics ; Ligands ; Machine Learning ; Protein Binding ; Proteins/chemistry
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2022-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.2c00634
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Book ; Online ; Thesis: <dc:title>Developing a workflow management system for fragment-based virtual screening</dc:title>

Bray, Simon A. [Verfasser] / Backofen, Rolf [Akademischer Betreuer] / Backofen, Rolf / Wolf, Steffen

2023

Keywords	Biowissenschaften, Biologie ; Life Science, Biology
Subject code	sg570
Language	English
Publisher	Universität
Publishing place	Freiburg
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Book ; Online: Ligand unbinding pathway and mechanism analysis assisted by machine learning and graph methods

Bray, Simon / Tänzel, Victor / Wolf, Steffen

2022

Abstract	We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for reducing the dimensionality of the input data, followed by identification of unbinding paths and training a machine learning model for trajectory clustering. The second approach clusters trajectories according to their pairwise mean Euclidean distance employing the neighbor-net algorithm, which takes into account input data bias in the distances set and is superior to dendrogram construction. Finally, we describe a more complex case where the reaction coordinate relevant for path identification is a single intra-ligand hydrogen bond, highlighting the challenges involved in unbinding path reaction coordinate detection. Comment: This preprint is the unformatted version of a manuscript that has been submitted to a scientific publisher for consideration as an article in a scientific journal. Copyright will be with the publisher after publication
Keywords	Physics - Biological Physics ; Physics - Data Analysis ; Statistics and Probability ; Quantitative Biology - Biomolecules
Subject code	004
Publishing date	2022-05-19
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multisecond ligand dissociation dynamics from atomistic simulations.

Wolf, Steffen / Lickert, Benjamin / Bray, Simon / Stock, Gerhard

Nature communications

2020 Volume 11, Issue 1, Page(s) 2918

Abstract: Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and rate-limiting steps ...

Abstract	Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and rate-limiting steps in protein-ligand unbinding is crucial for modern drug discovery. To achieve the enhanced sampling, we perform dissipation-corrected targeted molecular dynamics simulations, which yield free energy and friction profiles of molecular processes under consideration. Subsequently, we use these fields to perform temperature-boosted Langevin simulations which account for the desired kinetics occurring on multisecond timescales and beyond. Adopting the dissociation of solvated sodium chloride, trypsin-benzamidine and Hsp90-inhibitor protein-ligand complexes as test problems, we reproduce rates from molecular dynamics simulation and experiments within a factor of 2-20, and dissociation constants within a factor of 1-4. Analysis of friction profiles reveals that binding and unbinding dynamics are mediated by changes of the surrounding hydration shells in all investigated systems.
MeSH term(s)	Benzamidines/chemistry ; Binding Sites ; Models, Theoretical ; Molecular Dynamics Simulation ; Protein Binding ; Sodium Chloride/chemistry ; Thermodynamics ; Trypsin/chemistry ; Water/chemistry
Chemical Substances	Benzamidines ; Water (059QF0KO0R) ; Sodium Chloride (451W47IQ8X) ; Trypsin (EC 3.4.21.4) ; benzamidine (KUE3ZY3J1F)
Language	English
Publishing date	2020-06-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-16655-1
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Article ; Online: Data on elemental concentrations in marine sediments from the South and South West of England.

Richir, Jonathan / Bray, Simon / McAleese, Tom / Watson, Gordon J

Data in brief

2021 Volume 35, Page(s) 106901

Abstract: The present Data In Brief methodological paper details the acquisition, mining and pre-processing of elemental concentration data in marine sediments (coastal and open sea) of Southern England, presented and discussed in the co-submitted Environment ... ...

Abstract	The present Data In Brief methodological paper details the acquisition, mining and pre-processing of elemental concentration data in marine sediments (coastal and open sea) of Southern England, presented and discussed in the co-submitted Environment International paper entitled: "Three decades of trace element sediment contamination: the mining of governmental databases and the need to address hidden sources for clean and healthy seas" [1]. Elemental sediment concentration data were obtained from the two main UK environmental sources, i.e. the Environment Agency (EA) and the Marine Environment Monitoring and Assessment National (MERMAN) database managed by the British Oceanographic Data Centre (BODC). The merged database is the result of a rigorous data selection-validation process and provides spatially and temporally extensive records of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn) concentrations for hundreds of sites over 31 years (1983-2013). Additional records of manganese (Mn), aluminium (Al), lithium (Li), tin (Sn) [and tributyltin (TBT)], barium (Ba), antimony (Sb), boron (B), calcium (Ca), molybdenum (Mo), cobalt (Co), selenium (Se), potassium (K), magnesium (Mg), beryllium (Be), vanadium (V), titanium (Ti), sodium (Na), silver (Ag), thallium (Tl) and strontium (Sr) are also included. The full secondary database is hosted in the Mendeley Data repository and the geo-spatial information to map sites is given in supplementary files to the paper. To provide end-users with the relevant context on spatial and temporal coverage, monitoring statistics are given for the nine trace elements (TEs). Site-specific statistics include: the first and last year of sediment monitoring, the number of years monitored, and minimum, maximum, mean and median numbers of years monitored. Also given are summary data on the number of sites monitored each year, from the first records from 1983 to 2013. For the nine TEs (total and strong acid digestion techniques are considered separately for Cr and Fe), monitoring statistics are presented separately for coastal and open sea sites. Data are relevant to diverse end-users to assess the local and regional contaminant loads and to contextualize anthropogenic threats to benthic systems in multiple locations from the French/English Channel, southern North and Celtic Seas.
Language	English
Publishing date	2021-02-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106901
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Article ; Online: Three decades of trace element sediment contamination: The mining of governmental databases and the need to address hidden sources for clean and healthy seas.

Richir, Jonathan / Bray, Simon / McAleese, Tom / Watson, Gordon J

Environment international

2021 Volume 149, Page(s) 106362

Abstract: Trace elements (TEs) frequently contaminate coastal marine sediments with many included in priority chemical lists or control legislation. These, improved waste treatment and increased recycling have fostered the belief that TE pollution is declining. ... ...

Abstract	Trace elements (TEs) frequently contaminate coastal marine sediments with many included in priority chemical lists or control legislation. These, improved waste treatment and increased recycling have fostered the belief that TE pollution is declining. Nevertheless, there is a paucity of long-term robust datasets to support this confidence. By mining UK datasets (100s of sites, 31 years), we assess sediment concentrations of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn) and use indices (PI [Pollution], TEPI [Trace Element Pollution] and I
MeSH term(s)	Environmental Monitoring ; Geologic Sediments ; Metals, Heavy/analysis ; Oceans and Seas ; Risk Assessment ; Trace Elements/analysis ; Water Pollutants, Chemical/analysis
Chemical Substances	Metals, Heavy ; Trace Elements ; Water Pollutants, Chemical
Language	English
Publishing date	2021-02-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	554791-x
ISSN	1873-6750 ; 0160-4120
ISSN (online)	1873-6750
ISSN	0160-4120
DOI	10.1016/j.envint.2020.106362
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Article: Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.

Bray, Simon / Dudgeon, Tim / Skyner, Rachael / Backofen, Rolf / Grüning, Björn / von Delft, Frank

Journal of cheminformatics

2022 Volume 14, Issue 1, Page(s) 22

Abstract: We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on ...

Abstract	We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 50000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.
Language	English
Publishing date	2022-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2486539-4
ISSN	1758-2946
ISSN	1758-2946
DOI	10.1186/s13321-022-00588-6
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Article: Data on elemental concentrations in marine sediments from the South and South West of England

Richir, Jonathan / Bray, Simon / McAleese, Tom / Watson, Gordon J.

Data in Brief. 2021 Apr., v. 35

2021

Abstract	The present Data In Brief methodological paper details the acquisition, mining and pre-processing of elemental concentration data in marine sediments (coastal and open sea) of Southern England, presented and discussed in the co-submitted Environment International paper entitled: “Three decades of trace element sediment contamination: the mining of governmental databases and the need to address hidden sources for clean and healthy seas” [1]. Elemental sediment concentration data were obtained from the two main UK environmental sources, i.e. the Environment Agency (EA) and the Marine Environment Monitoring and Assessment National (MERMAN) database managed by the British Oceanographic Data Centre (BODC). The merged database is the result of a rigorous data selection-validation process and provides spatially and temporally extensive records of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn) concentrations for hundreds of sites over 31 years (1983–2013). Additional records of manganese (Mn), aluminium (Al), lithium (Li), tin (Sn) [and tributyltin (TBT)], barium (Ba), antimony (Sb), boron (B), calcium (Ca), molybdenum (Mo), cobalt (Co), selenium (Se), potassium (K), magnesium (Mg), beryllium (Be), vanadium (V), titanium (Ti), sodium (Na), silver (Ag), thallium (Tl) and strontium (Sr) are also included. The full secondary database is hosted in the Mendeley Data repository and the geo-spatial information to map sites is given in supplementary files to the paper. To provide end-users with the relevant context on spatial and temporal coverage, monitoring statistics are given for the nine trace elements (TEs). Site-specific statistics include: the first and last year of sediment monitoring, the number of years monitored, and minimum, maximum, mean and median numbers of years monitored. Also given are summary data on the number of sites monitored each year, from the first records from 1983 to 2013. For the nine TEs (total and strong acid digestion techniques are considered separately for Cr and Fe), monitoring statistics are presented separately for coastal and open sea sites. Data are relevant to diverse end-users to assess the local and regional contaminant loads and to contextualize anthropogenic threats to benthic systems in multiple locations from the French/English Channel, southern North and Celtic Seas.
Keywords	aluminum ; antimony ; arsenic ; barium ; beryllium ; boron ; cadmium ; calcium ; chromium ; cobalt ; copper ; databases ; iron ; lead ; lithium ; magnesium ; manganese ; marine environment ; mercury ; molybdenum ; nickel ; paper ; potassium ; sediment contamination ; selenium ; silver ; sodium ; statistics ; strontium ; thallium ; tin ; titanium ; tributyltin ; vanadium ; wet digestion method ; zinc ; England ; English Channel
Language	English
Dates of publication	2021-04
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106901
Database	NAL-Catalogue (AGRICOLA)

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Article: Three decades of trace element sediment contamination: The mining of governmental databases and the need to address hidden sources for clean and healthy seas

Richir, Jonathan / Bray, Simon / McAleese, Tom / Watson, Gordon J

Environment international. 2021 Apr., v. 149

2021

Abstract	Trace elements (TEs) frequently contaminate coastal marine sediments with many included in priority chemical lists or control legislation. These, improved waste treatment and increased recycling have fostered the belief that TE pollution is declining. Nevertheless, there is a paucity of long-term robust datasets to support this confidence. By mining UK datasets (100s of sites, 31 years), we assess sediment concentrations of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), mercury (Hg), nickel (Ni), lead (Pb) and zinc (Zn) and use indices (PI [Pollution], TEPI [Trace Element Pollution] and Igₑₒ [Geoaccumulation]) to assess TE pollution evolution. PI and TEPI show reductions of overall TE pollution in the 1980s then incremental improvements followed by a distinct increase (2010–13). Zn, As and Pb Igₑₒ scores show low pollution, whilst Cd and Hg are moderate, but with all remaining temporally stable. Igₑₒ scores are low for Ni, Fe and Cr, but increasing for Ni and Fe. A moderate pollution Igₑₒ score for Cu has also steadily increased since the mid-1990s. Increasing site trends are not universal and, conversely, minimal temporal change masks some site-specific increases and decreases. To capture this variability we strongly advocate embedding sufficient sentinel sites within observation networks. Decreasing sediment pollution levels (e.g. Pb and Hg) have been achieved, but stabilizing Igₑₒ and recently increasing TEPI and PI scores require continued global vigilance. Increasing Ni and Fe Igₑₒ scores necessitate source identification, but this is a priority for Cu. Local, regional and world analyses indicate substantial ‘hidden’ inputs from anti-fouling paints (Cu, Zn), ship scrubbers (Cu, Zn, Ni) and sacrificial anodes (Zn) that are also predicted to increase markedly. Accurate TE input assessments and targeted legislation are, therefore, urgently required, especially in the context of rapid blue economic growth (e.g. shipping).
Keywords	arsenic ; cadmium ; chromium ; copper ; data collection ; economic development ; environment ; iron ; laws and regulations ; lead ; mercury ; nickel ; sediment contamination ; temporal variation ; waste treatment ; zinc
Language	English
Dates of publication	2021-04
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	554791-x
ISSN	1873-6750 ; 0160-4120
ISSN (online)	1873-6750
ISSN	0160-4120
DOI	10.1016/j.envint.2020.106362
Database	NAL-Catalogue (AGRICOLA)

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