ProteinsPlus should be referenced with the URL https://proteins.plus and the following citation: Sch\xf6ning-Stierand, K.; Diedrich, K.; Ehrt, C.; Flachsenberg, F.; Graef, J.; Sieg, J.; Penner, P.; Poppinga, M.; Ungeth\xfcm, A.; Rarey, M. (2022). ProteinsPlus: a comprehensive collection of web-based molecular modeling tools..
What are the applications of protein?
Proteins are very essential for the structural and functional growth of the body. They are thee polymer of amino acid linked by covalent bonds. Proteins and peptides are widely used as pharmaceutical agents in antiviral agents, antibiotic, as prodrug and even antimicrobial agent..
What are the biological applications of protein models?
Protein structure modeling can be applied to determine protein-protein interaction prediction, protein-protein docking, molecular docking, and functional annotation of genes identified in the organism's genome..
What is protein in bioinformatics?
Proteins are molecular devices, in the nanometer scale, where biological function is exerted (1). They are the building blocks of all cells in our bodies and in all living creatures of all kingdoms..
What is the application of bioinformatics in protein structure?
Protein structure prediction by using bioinformatics can involve sequence similarity searches, multiple sequence alignments, identification and characterization of domains, secondary structure prediction, solvent accessibility prediction, automatic protein fold recognition, constructing three-dimensional models to .
Why are proteins studied?
Individual proteins have a defined shape and structure. Proteins work together in a complicated and coordinated way to support our life. In other words, understanding the functions of proteins could give us hints to answer the question "What is life?" and observing the structures in detail could reveal how they work..
Why is it important to study protein parameters?
Each of these parameters provides valuable information about protein characterization. Insights from protein stability analyses improve understanding and outcomes for protein activity, binding partners, kinetics, drug development, and more..
Why is the study of proteins important?
Individual proteins have a defined shape and structure. Proteins work together in a complicated and coordinated way to support our life. In other words, understanding the functions of proteins could give us hints to answer the question "What is life?" and observing the structures in detail could reveal how they work..
A DoGSiteScorer calculation results in a list of potential pocket of the given structure and additional information on pocket characteristics listed in a result table. Each row represents a certain pocket and its features.
Individual proteins have a defined shape and structure. Proteins work together in a complicated and coordinated way to support our life. In other words, understanding the functions of proteins could give us hints to answer the question "What is life?" and observing the structures in detail could reveal how they work.
Protein structure modeling can be applied to determine protein-protein interaction prediction, protein-protein docking, molecular docking, and functional annotation of genes identified in the organism's genome.
ProteinsPlus has its focus on protein-ligand interactions. The server provides support for the initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing.
The aim of ProteinsPlus is to support life scientists in working with protein structures1,2,3. Protein structures are the key for an understanding of function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis.
Geomine
From the analysis of binding sites to investigations of geometric preferences for interactions, the ever-increasing number of molecular structures in the PDB offers a multitude of possibilities for in-depth studies of binding sites, their properties and their similarities. This requires comprehensive search capabilities. With GeoMine (5,6), we have.
Integration of Alphafold Structures
The inclusion of AlphaFold protein structure models (4) (https://alphafold.ebi.ac.uk/) in the ProteinsPlus web server enables easy access to machine learning-based predictions of previously unknown structures. The models are accessible on our web server by entering the UniProt Accession Number on the landing page or uploading a preprocessed structu.
Jamda
Protein–ligand docking is one of the core tasks in structure-based drug design. With JAMDA, we aimed for the implementation of a fully-automated docking workflow in the ProteinsPlus server that does not only provide the actual docking algorithm but also encompasses all necessary preprocessing steps, including protonation state assignment and calcul.
Microminer
MicroMiner searches for mutations in protein structure databases. On ProteinsPlus, it screens for single-residue substitutions in the experimental structures of the entire PDB. Retrieved mutant structures can be easily analyzed and compared to the wildtype through automatically generated superpositions in the NGL viewer. The tool focuses on the loc.
What is proteins plus?
The aim of Proteins Plus is to support life scientists in working with protein structures 1,2,3 . Protein structures are the key for an understanding of function. They are an important resource in many biotechnological application areas from pharmaceutical research to biocatalysis. Proteins Plus has its focus on protein-ligand interactions.
What is proteinsplus based modeling support server?
For more information, please refer to our privacy policy . ProteinsPlus structure-based modeling support server. This server is a common web portal for all tools related to structure-based modeling created by the AMD group (Prof. M. Rarey) at ZBH, Hamburg, including:
DoGSite Scorer
EDIA
PPI
PoseView
SIENA and ProToss .
What tools are supported by proteins plus?
Furthermore, advanced options, such as:
protein pocket detection
ensemble generation or prediction of metal coordinations are supported. All tools are developed in the Computational Molecular Design Group (AMD) headed by Matthias Rarey . Currently, Proteins Plus allows you to:.
Who develops the Protein Plus web service?
The development of the Proteins Plus web service is supported by the BMBF as part of de.NBI – German Network for Bioinformatics Infrastructure. Its use is free for academic and commercial purposes – we thank you for citing the Proteins Plus and the computational methods behind it.
The AMRFinderPlus tool from the National Center for Biotechnology Information (NCBI) is a bioinformatic tool that allows users to identify antimicrobial resistance determinants, stress response, and virulence genes in bacterial genomes. This tool's development began in 2018 and is still underway. The National Institutes of Health funds the development of the software and the databases it uses.
Protein plus bioinformatics
Sequencing of amino acid arrangement in a protein
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information to identify it with reference to databases of protein sequences derived from the conceptual translation of genes.
Transmembrane protein 251, also known as C14orf109 or UPF0694, is a protein that in humans is encoded by the TMEM251 gene. One notable feature of this protein is the presence of proline residues on one of its predicted transmembrane domains., which is a determinant of the intramitochondrial sorting of inner membrane proteins.
The AMRFinderPlus tool from the National Center for Biotechnology Information (NCBI) is a bioinformatic tool that allows users to identify antimicrobial resistance determinants, stress response, and virulence genes in bacterial genomes. This tool's development began in 2018 and is still underway. The National Institutes of Health funds the development of the software and the databases it uses.
Protein sequencing is the practical process of determining the amino acid
Sequencing of amino acid arrangement in a protein
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information to identify it with reference to databases of protein sequences derived from the conceptual translation of genes.
Transmembrane protein 251, also known as C14orf109 or UPF0694, is a protein that in humans is encoded by the TMEM251 gene. One notable feature of this protein is the presence of proline residues on one of its predicted transmembrane domains., which is a determinant of the intramitochondrial sorting of inner membrane proteins.
