Structural Genomics, Part C: 77 (Advances in Protein Chemistry and Structural Biology)
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It became clear that in order for the biological community to get the maximum benefit from the products of the PSI effort, a single centralized website was needed. In February , the Structural Genomics Knowledgebase [ 4 ] was created which combined the PSI products with data from publicly available biological resources in order to show comprehensive information, including experimental data prior to publication, to jumpstart biological research.
It also improved features to foster collaborations between the biological community and the PSI. In this article, we describe all of the features available on the SBKB that can be used to enable biological research, and present some examples of its use. The SBKB homepage provides entry points to the following content and functionalities:.
These menu items give facile access to topics relevant to the biological and biomedical research, such as resources for target, structure, methods, models, and publication information.
Advances in Protein Chemistry and Structural Biology
This section of the SBKB provides a collection of recent research and technical highlights from the PSI and broader structural biology community, news, upcoming events, and a research library of PSI and other structural biology articles provided by the NPG. A new molecule is selected each month. Text searches will also return matching highlights published as part of the Structural Biology Update. Users can subscribe to a monthly electronic Table of Contents alert service e-alert on Nature.
The PSI:Biology Network invites the biological community to nominate proteins of biological relevance for structural determination. This proposal system begins the process of matching your project with one of 13 high-throughput and membrane protein structure determination centers to carry out the study. The Sequence Comparison and Analysis SCA tool consists of the same functionality as the Community-Nominated Target proposal system described previously, but provides an evaluation report to the author only rather than forwarding it to a selection committee.
It also supports batch submission to evaluate s of sequences. Functional Sleuth enables further research for proteins in the Protein Data Bank archive whose functions are unknown or minimally characterized.
You can download a comma-separated-variable. This feature is updated weekly in conjunction with the weekly PDB release. The PSI Network tracks its measure of success and progress though a series of agreed metrics. These metrics, including statistics such as the number of protein structures solved and calculated modeling leverage, were defined by the Goals and Metrics Committee for the PSI-2 Network.
BioSync provides technical details about structural biology beamlines at synchrotron radiation facilities. Progress on future facilities is tracked and information on decommissioned sites is maintained for historical purposes. Links are also provided to related external resources. Summary statistics, based on PDB depositions, are produced and updated weekly.
At the beamline level, galleries of structures, tables of citations and general information are also available. Separate statistics are provided for structures solved by structural genomics efforts. This site can be found on the methods hub page from the left navigation menu. These tutorials not only introduce new users to the SBKB, but also give lessons on how to interpret the data being presented. List of web addresses to access the features and underlying portals of the Structural Biology Knowledgebase. We describe the resources used in SBKB query and reporting mechanism in the context of commonly used examples.
If a 3D structure exists for a protein of interest, the SBKB currently utilizes the molecular viewer FirstGlance [ ] to explore the molecule and binding partners other proteins, ligands, nucleic acids, etc.
The SBKB manages two databases that track structural genomics efforts. This information includes sequence and site information, target experimental status, and timestamps for the latest experimental step cloned, expressed, purified, etc. It currently holds over 40, PSI plasmids and nearly empty vectors available for request with an additional PSI plasmids added on a monthly basis. If a sequence search yielded no experimental structures for the protein of interest, there are other sources of information to help design future experiments:.
Example of a Protein Model Portal model comparison analysis. The current release Mar consists of Queries can be entered as protein sequences in one-letter code or UniProt accession IDs. Results are presented in a graphical and intuitive way, indicating regions of the proteins where structural information experimental or theoretical is available, complemented with functional and domain annotation. Graphs and images that display and assess model quality and reliability are available, and are an essential component to allow users to select the best available structural information for a specific application.
Example of a Sequence Analysis report.
Advances in automated NMR protein structure determination
It will also submit the sequence to the PSI-developed XtalPred and Pxs servers to calculate biophysical parameters and crystallization propensities. In this example, the given sequence was calculated to be a class 4 difficulty hard , so further construct optimization may be required to ensure a successful structure determination.
The PSI centers have developed and utilized many technologies that facilitated structural determination and analysis. A text search of the SBKB allows a user to find these methods. Reports can be queried by text, by PSI center, or by clicking an image of an experimental pipeline diagram. These articles are organized by topic structural or methodological or by PSI center, and can be searched by author, title, journal, PDB ID, or other attributes.
As part of the Structural Biology update, SBKB and Nature editors add articles published by leading scientific journals that relate to structural biology and structural genomic.
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Articles are organized into subjects that range from cloning to automated annotation, it should be noted that the articles listed here will require subscription to the relevant journals. The methods articles from this series summarized the latest strategies developed for protein isolation and structural determination methods.
The SBKB uses an architecture that collects IDs and selected annotations into a central portal database that is organized to facilitate queries and the addition of new annotations. Each of the SBKB portals developed their underlying architectures with guidelines for common protocols that would allow for easy data exchange with the central SBKB. These sets were then used to carry out fold cross-validation and evaluate the performance of our predictor PhoglyStruct. We obtained eight properties corresponding to the accessible surface area, backbone torsion angles, and secondary structure for each amino acid in the protein sequences.
The SPIDER2 toolbox is known to achieve good results regarding the prediction of the accessible surface area 45 , 46 , 47 , secondary structure 48 , 49 and backbone torsion angles 45 , 50 in proteins. It has also been reported for successful extraction of structural properties of proteins for sequence-based binding sites prediction 51 , These features are considered important source to provide information about the local interaction of amino acids along the protein sequence. Also, they have been used in different studies to tackle different problems in protein science and attained promising results 53 , 54 , 55 , The subsequent sections below discuss these structural properties.
Exploration of Uncharted Regions of the Protein Universe
The estimate of the accessible area of an amino acid to a solvent in the 3D configuration of a protein is given by ASA 57 , Hence, essential information on the protein structure is revealed by the predicted ASA of individual amino acids. It is worthwhile to mention that SPIDER2 uses only the primary sequence of proteins, so the prediction is entirely based on sequence information.
Secondary structure gives the information on the local 3D structure of proteins. For each amino acid, the predicted secondary structure provides a discrete output of its contribution to one of the three defined local structures of a protein which are coil, strand, and helix. This matrix is called SS pre for simplicity. Torsion angles, which are the angles between neighboring amino acids, complements ASA as well as the predicted secondary structure by providing important, continuous information about the local structure of amino acids Here we will discuss the feature extraction method for each of the lysine residues.
The 2 upstream and 2 downstream amino acids neighboring the lysine residue K is indicated in Fig. For the cases where the lysine residue did not have two neighboring amino acids, either upstream or downstream, the missing amino acids were created using the mirror effect 53 as shown in Fig. Illustration of the arrangement of neighboring amino acids to the lysine residue. Left mirroring for inadequate upstream and right mirroring for insufficient downstream amino acids.
The peptide sequence comprising 2 upstream and 2 downstream amino acids, including lysine residue K at the center, can be expressed as:. It can be deduced from equation 1 that a total of 5 amino acids, including lysine K , represent a lysine residue. Moreover, each amino acid in peptide P is described by the structural properties as denoted by equation 2 :. These properties are numeric, so each feature consists of a single value.
A Multilayer Perceptron network has three main components namely the input layer, a hidden layer, and an output layer.
go Input signals to the network propagate layer-by-layer. Despite the disadvantage of tuning a number of parameters such as the number of hidden neurons, it can learn highly non-linear models. The network computes an output by mapping the weighted combination of inputs through its hidden layer of nodes using a nonlinear activation function.
In this work, we utilized the Weka software to generate the MLP with sigmoid function An architectural representation of the multilayer perceptron is shown in Fig. We have used a successive feature selection SFS technique to rank and select amino acid properties, out of the eight proposed in this work, which actually contribute towards the identification of phosphoglycerylation and non-phosphoglycerylation sites. The SFS scheme utilized for this purpose is called backward elimination In this method, the group of features which belong to a property is eliminated at each successive levels from the feature set.
The feature set of the removed property, which resulted in the highest average G-Mean using fold cross-validation on the multilayer perceptron classifier was progressed to the next subsequent level.
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The elimination of a property at each of the levels causes the feature set size to reduce by 5 values for 5 amino acids corresponding to the property as the network is progressed.