Brian W. Matthews
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View article: D1.2 Data Management Plan
D1.2 Data Management Plan Open
This deliverable is the first version of the FAIRsFAIR Data Management Plan (DMP). It contains an initial description of the datasets (to be) collected, processed or generated by the project and an initial plan on how sharing, archiving an…
View article: D1.2 Data Management Plan
D1.2 Data Management Plan Open
This deliverable is the first version of the FAIRsFAIR Data Management Plan (DMP). It contains an initial description of the datasets (to be) collected, processed or generated by the project and an initial plan on how sharing, archiving an…
View article: ExPaNDS Librarian Symposium Report and presentations
ExPaNDS Librarian Symposium Report and presentations Open
This report follows the stakeholder engagement strategy where the event was focused on our Librarians and data managers and highlights the discussion points and key insights gained during the webinar. It also contains PDF copies of the pre…
View article: Recognizing lysine–cysteine crosslinks in proteins
Recognizing lysine–cysteine crosslinks in proteins Open
Recently, Tittmann and coworkers1 reported a protein structure in which a lysine and a cysteine are crosslinked via a N─O─S bridge. An accompanying News and Views commentary2 stated that “such N─O─S bridges have gone unnoticed in previousl…
View article: Translating the Molecules: Adapting Neural Machine Translation to Predict IUPAC Names from a Chemical Identifier
Translating the Molecules: Adapting Neural Machine Translation to Predict IUPAC Names from a Chemical Identifier Open
We present a sequence-to-sequence machine learning model for predicting the IUPAC name of a chemical from its standard International Chemical Identifier (InChI). The model uses two stacks of transformers in an encoder-decoder architecture,…
View article: <i>Protein Science</i> best papers for 2020
<i>Protein Science</i> best papers for 2020 Open
Protein Science, the flagship journal of The Protein Society, serves an international forum for publishing original reports on all scientific aspects of protein molecules. The Journal publishes papers by leading scientists from all over th…
View article: Additional file 3 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
Additional file 3 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier Open
Additional file 3. InChI character vocabulary needed for training the model with OpenNMT.
View article: Additional file 2 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
Additional file 2 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier Open
Additional file 2. Training script for OpenNMT-py.
View article: Additional file 4 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
Additional file 4 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier Open
Additional file 4. IUPAC character vocabulary needed for training the model with OpenNMT.
View article: Additional file 1 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier
Additional file 1 of Translating the InChI: adapting neural machine translation to predict IUPAC names from a chemical identifier Open
Additional file 1. 100 molecule test set including InChI and IUPAC names from PubChem, ACD /I-Labs, ChemAxon, Mestrelab and the transformer presented in the current paper.
View article: Tools 2021: New methods, new approaches, and a salute to recent developments in protein science
Tools 2021: New methods, new approaches, and a salute to recent developments in protein science Open
It is now 3 years since we published our first “Tools” special issue. The outstanding success of that issue, in January 2018, prompted us to publish a follow-up issue 12 months ago. The present release, Tools 2021, is the third in the seri…
View article: <i>Protein Science</i> best paper awards to Yu‐ming Huang and Abhay Thakur
<i>Protein Science</i> best paper awards to Yu‐ming Huang and Abhay Thakur Open
Warmest congratulations to Yu-ming “Mindy” Huang1 and Abhay Thakur2 (Fig. 1), recipients of the Protein Society's Year 2018 “Best Paper” awards. At the beginning of each year, two “best papers” are selected from articles published in Prote…
View article: <i>Protein Science</i> best paper awards to Minfei Su and Chang‐Ting Lin
<i>Protein Science</i> best paper awards to Minfei Su and Chang‐Ting Lin Open
Warmest congratulations to Minfei Su1 and Chang-Ting Lin2 (Figure 1), the recipients of the Protein Society's Year 2017 “Best Paper” awards. Award winners. (A) Minfei Su. (B) Chang-Ting Lin. At the beginning of each year, two “best papers”…
View article: Tools for protein science
Tools for protein science Open
When I started as a Ph.D. student in Australia in 1961, no one in our department, or for that matter in the entire University of Adelaide, had a computer. All of our calculations had to be done by hand. Determining a projection electron de…
View article: Issue information
Issue information Open
View article: David Davies: Structural biologist and mentor
David Davies: Structural biologist and mentor Open
David Davies (Fig. 1) was not, initially, a macromolecular crystallographer and neither was he enthusiastic about the prospects of using crystallography to determine the structures of proteins. During the time that he was a student at Oxfo…
View article: Issue information ‐ Copyright and Table of Contents
Issue information ‐ Copyright and Table of Contents Open
View article: Issue information ‐ Copyright and Table of Contents
Issue information ‐ Copyright and Table of Contents Open
View article: <i>Protein Science</i> best paper awards to Tracy Clinton and Michael Thompson
<i>Protein Science</i> best paper awards to Tracy Clinton and Michael Thompson Open
Warmest congratulations to Tracy Clinton1 and Michael Thompson2 (Fig. 1), the recipients of the Protein Society's Year 2015 “Best Paper” awards. Award winners. A: Tracy Clinton. B: Michael Thompson. At the beginning of each year, two “best…
View article: Issue information ‐ Copyright and Table of Contents
Issue information ‐ Copyright and Table of Contents Open
View article: How planar are planar peptide bonds?
How planar are planar peptide bonds? Open
One of the best-known blunders in the history of molecular biology was the assumption of Bragg, Kendrew, and Perutz that peptide bonds are non-planar, leading to their incorrect predictions for helical structures in proteins. Conversely, P…
View article: Issue Information
Issue Information Open
View article: Issue Information
Issue Information Open
View article: Issue Information
Issue Information Open
View article: Issue Information
Issue Information Open
View article: How do I know that I have preserved software?
How do I know that I have preserved software? Open
Software is a class of digital electronic object which is often a prerequisite to the preservation of other electronic objects. However, software has characteristics that make its preservation substantially more challenging than many other…
View article: Issue Information
Issue Information Open
View article: Issue Information
Issue Information Open
View article: <i>Protein Science</i> Best Paper awards to Chih‐Chia (Jack) Su and Minttu Virkki
<i>Protein Science</i> Best Paper awards to Chih‐Chia (Jack) Su and Minttu Virkki Open
Warmest congratulations to Jack Su and Minttu Virkki (Figure 1), the recipients of the Protein Society's Year 2014 “Best Paper” awards. Award winners. (A) Chih-Chia (Jack) Su. (B) Minttu Virkki. At the beginning of each year, two “best pap…
View article: Which of the 100,000 structures in the protein data bank are reliable?
Which of the 100,000 structures in the protein data bank are reliable? Open
There are at present over 100,000 protein structures in the Protein Data Bank. Suppose you are particularly interested in a certain entry. How can you determine its quality? Traditionally, the so-called R-factor has been used for this purp…