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
Impact of the removal of N-terminal non-structured amino acids on activity and stability of xylanases from Orpinomyces sp. PC-2.
Rafaela Zandonade Ventorim,Tiago Antônio de Oliveira Mendes,Larissa Mattos Trevizano,Ana Maria dos Santos Camargos,Valéria Monteze Guimarães +4 more
TL;DR: It is proposed that the presence of non-structured amino acid in the N-terminal leads to destabilization of the xylanases and may promote less access of the substrate to the active site and its removal may promote increased stability and enzymatic activity, interesting properties that make them suitable for biotechnological applications.
Journal ArticleDOI
Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19
E.K. Oladipo,E.K. Oladipo,Ayodeji Folorunsho Ajayi,Olumuyiwa Elijah Ariyo,Samson Olugbenga Onile,Esther Moradeyo Jimah,Esther Moradeyo Jimah,Louis Odinakaose Ezediuno,Louis Odinakaose Ezediuno,Oluwadunsin Iyanuoluwa Adebayo,Oluwadunsin Iyanuoluwa Adebayo,Emmanuel Tayo Adebayo,Emmanuel Tayo Adebayo,Aduragbemi Noah Odeyemi,Aduragbemi Noah Odeyemi,Marvellous Oluwaseun Oyeleke,Moyosoluwa Precious Oyewole,Ayomide Samuel Oguntomi,Olawumi Elizabeth Akindiya,Bunmi Olayemi Olamoyegun,Victoria Oyetayo Aremu,Victoria Oyetayo Aremu,Abiola O. Arowosaye,Dorcas Olubunmi Aboderin,Habibat Bolanle Bello,Tosin Yetunde Senbadejo,E.H. Awoyelu,A.A. Oladipo,Bukola Bisola Oladipo,Lydia Oluwatoyin Ajayi,Olusola Nathaniel Majolagbe,Olubukola Monisola Oyawoye,Julius Kola Oloke +32 more
TL;DR: Results obtained indicated that this novel vaccine candidate is non-toxic, capable of initiating the immunogenic response and will not induce an allergic reaction, and awaits animal trial to validate its efficacy and safety for use in the prevention of the novel COVID-19 infections.
Journal ArticleDOI
Interactive role of salicylic acid and nitric oxide on transcriptional reprogramming for high temperature tolerance in lablab purpureus L.: Structural and functional insights using computational approaches.
TL;DR: Combined effect of SA and NO enhances tolerance in HT stressed L. purpureus by regulating physiological functions, antioxidants, expression and regulation of stress-responsive genes via transcriptional regulation of heat shock factor.
Journal ArticleDOI
SARS CoV-2 Spike Protein in silico Interaction With ACE2 Receptors From Wild and Domestic Species
Santiago Rendon-Marin,Marlen Martinez-Gutierrez,Gary R. Whittaker,Javier A. Jaimes,Julian Ruiz-Saenz +4 more
TL;DR: In this article, the authors performed a protein-protein molecular docking analysis of SARS-CoV-2 spike protein with the ACE2 receptor from different animals to elucidate the potential of those species as intermediate hosts or susceptible animals for SARS CoV2 infection.
Journal ArticleDOI
Design and characterization of a new hybrid peptide from LL-37 and BMAP-27.
Yara Al Tall,Ahmad Abualhaijaa,Mohammad Alsaggar,Ammar Almaaytah,Majed M Masadeh,Karem H. Alzoubi +5 more
TL;DR: A hybrid antimicrobial peptide (B1) from helical parts taken from the parent peptides: LL-37 and BMAP-27 showed an improved activity compared to parent peptide, and the synergism with the convention antibiotics showed promising results.
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.