ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.
Reads0
Chats0
TLDR
The quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer in the ProSA-web service.Abstract:
A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.read more
Citations
More filters
Journal ArticleDOI
Chimeric Vaccines Designed by Immunoinformatics-Activated Polyfunctional and Memory T Cells That Trigger Protection against Experimental Visceral Leishmaniasis
Rory Cristiane Fortes de Brito,Jeronimo C. Ruiz,Jamille Mirelle de Oliveira Cardoso,Thais Lopes Valentim Di Paschoale Ostolin,Levi Eduardo Soares Reis,Fernando Augusto Siqueira Mathias,Rodrigo Dian de Oliveira Aguiar-Soares,Bruno Mendes Roatt,Rodrigo Correa-Oliveira,Daniela de Melo Resende,Alexandre Barbosa Reis +10 more
TL;DR: Results showed that in silico-designed chimeras can elicit polyfunctional T cells producing T helper (Th)1 cytokines, a strong immune response against Leishmania antigen, and the generation of central and effector memory T cells in the spleen cells of vaccinated animals that was able to reduce the parasite burden in this organ.
Journal ArticleDOI
Computer aided subunit vaccine design against pathogenic Leptospira serovars
TL;DR: Cation efflux system membrane protein (czcA) and its four subunit vaccine peptides would be ideal T-cell driven efficacious vaccine against leptospirosis.
Journal ArticleDOI
Identification of small molecule inhibitors against SecA of Candidatus Liberibacter asiaticus by structure based design.
TL;DR: Five compounds were found to inhibit the ATPase activity of SecA of Las at nano molar concentrations and showed antimicrobial activities against Agrobacterium tumefaciens with MBC ranging from 128 to 256 μg/mL.
Journal ArticleDOI
Identification, structure analysis, and transcript profiling of purple acid phosphatases under Pi deficiency in tomato (Solanum lycopersicum L.) and its wild relatives.
TL;DR: It is demonstrated that the magnitude of induction of phosphate starvation inducible root-associated PAP homologs remains lower in the Pi-starved S. pimpinellifolium seedlings, hence, accounting for the lower acid phosphatase activity in this wild relative.
Journal ArticleDOI
Integrative binding sites within intracellular termini of TRPV1 receptor.
Lenka Grycova,Blanka Holendová,Ladislav Bumba,Jan Bily,Michaela Jirku,Zdenek Lansky,Jan Teisinger +6 more
TL;DR: Restraint-based molecular modeling combined with ligand docking was performed providing structural insight to the TRPV1/PIP2 binding, and the experimental results are in excellent agreement with in silico predictions.
References
More filters
Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Recognition of errors in three‐dimensional structures of proteins
TL;DR: Techniques based on knowledge based mean fields which can be used to judge the quality of protein folds are presented, used to identify misfolded structures as well as faulty parts of structural models.
Journal ArticleDOI
Structure of a bacterial multidrug ABC transporter
TL;DR: The observed, outward-facing conformation reflects the ATP-bound state, with the two nucleotide-binding domains in close contact and the two transmembrane domains forming a central cavity—presumably the drug translocation pathway—that is shielded from the inner leaflet of the lipid bilayer and from the cytoplasm, but exposed to the outer leaflet and the extracellular space.
Journal ArticleDOI
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.
TL;DR: A prototype of a new approach to the folding problem of polypeptide chains based on the analysis of known protein structures, which derives the energy potentials for the atomic interactions of all amino acid residue pairs as a function of the distance between the involved atoms is presented.
Journal ArticleDOI
Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters
TL;DR: The structure of MsbA can serve as a model for the MDR-ABC transporters that confer multidrug resistance to cancer cells and infectious microorganisms.