Dataset Information

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

ABSTRACT: The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

SUBMITTER: Niklasson M

PROVIDER: S-EPMC4288728 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Niklasson Markus M Ahlner Alexandra A Andresen Cecilia C Marsh Joseph A JA Lundström Patrik P

PLoS computational biology 20150108 1

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assig ...[more]

PMID: 25569628

Similar Datasets

Project description:Aim of Study: The use of weighed food diaries in nutritional studies provides a powerful method to quantify food and nutrient intakes. Yet, mapping these records onto food composition tables (FCTs) is a challenging, time-consuming and error-prone process. Experts make this effort manually and no automation has been previously proposed. Our study aimed to assess automated approaches to map food items onto FCTs. Methods: We used food diaries (~170,000 records pertaining to 4,200 unique food items) from the DiOGenes randomized clinical trial. We attempted to map these items onto six FCTs available from the EuroFIR resource. Two approaches were tested: the first was based solely on food name similarity (fuzzy matching). The second used a machine learning approach (C5.0 classifier) combining both fuzzy matching and food energy. We tested mapping food items using their original names and also an English-translation. Top matching pairs were reviewed manually to derive performance metrics: precision (the percentage of correctly mapped items) and recall (percentage of mapped items). Results: The simpler approach: fuzzy matching, provided very good performance. Under a relaxed threshold (score > 50%), this approach enabled to remap 99.49% of the items with a precision of 88.75%. With a slightly more stringent threshold (score > 63%), the precision could be significantly improved to 96.81% while keeping a recall rate > 95% (i.e., only 5% of the queried items would not be mapped). The machine learning approach did not lead to any improvements compared to the fuzzy matching. However, it could increase substantially the recall rate for food items without any clear equivalent in the FCTs (+7 and +20% when mapping items using their original or English-translated names). Our approaches have been implemented as R packages and are freely available from GitHub. Conclusion: This study is the first to provide automated approaches for large-scale food item mapping onto FCTs. We demonstrate that both high precision and recall can be achieved. Our solutions can be used with any FCT and do not require any programming background. These methodologies and findings are useful to any small or large nutritional study (observational as well as interventional).

Project description:New chest compression detection technology allows for the recording and graphical depiction of clinical cardiopulmonary resuscitation (CPR) chest compressions. The authors sought to determine the inter-rater reliability of chest compression pattern classifications by human raters. Agreement with automated chest compression classification was also evaluated by computer analysis.This was an analysis of chest compression patterns from cardiac arrest patients enrolled in the ongoing Resuscitation Outcomes Consortium (ROC) Continuous Chest Compressions Trial. Thirty CPR process files from patients in the trial were selected. Using written guidelines, research coordinators from each of eight participating ROC sites classified each chest compression pattern as 30:2 chest compressions, continuous chest compressions (CCC), or indeterminate. A computer algorithm for automated chest compression classification was also developed for each case. Inter-rater agreement between manual classifications was tested using Fleiss's kappa. The criterion standard was defined as the classification assigned by the majority of manual raters. Agreement between the automated classification and the criterion standard manual classifications was also tested.The majority of the eight raters classified 12 chest compression patterns as 30:2, 12 as CCC, and six as indeterminate. Inter-rater agreement between manual classifications of chest compression patterns was ? = 0.62 (95% confidence interval [CI] = 0.49 to 0.74). The automated computer algorithm classified chest compression patterns as 30:2 (n = 15), CCC (n = 12), and indeterminate (n = 3). Agreement between automated and criterion standard manual classifications was ? = 0.84 (95% CI = 0.59 to 0.95).In this study, good inter-rater agreement in the manual classification of CPR chest compression patterns was observed. Automated classification showed strong agreement with human ratings. These observations support the consistency of manual CPR pattern classification as well as the use of automated approaches to chest compression pattern analysis.

Project description:BackgroundSince the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus; most notably, the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade.ResultsIn this article, we leverage the frequency chaos game representation (FCGR) and convolutional neural networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieved an $96.29\%$ overall accuracy, while a similar tool, Covidex, obtained a $77,12\%$ overall accuracy. As far as we know, our method is the first using deep learning and FCGR for intraspecies classification. Furthermore, by using some feature importance methods, CouGaR-g allows to identify k-mers that match SARS-CoV-2 marker variants.ConclusionsBy combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on random forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants.AvailabilityThe trained models can be tested online providing a FASTA file (with 1 or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.

Dataset Information

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Publications

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets