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
Role of Motif B Loop in Allosteric Regulation of RNA-Dependent RNA Polymerization Activity
TL;DR: X-ray crystallography of RdRPs trapped in multiple steps throughout the catalytic process, together with NMR data and molecular dynamics simulations, have shown that all polymerase regions contributing to conserved motifs required for substrate binding, catalysis and product release are highly flexible and some of them are predicted to display correlated motions.
Journal ArticleDOI
Molecular docking between human TMPRSS2 and SARS-CoV-2 spike protein: conformation and intermolecular interactions
Mushtaq Hussain,Nusrat Jabeen,Anusha Amanullah,Ayesha Ashraf Baig,Basma Aziz,Sanya Shabbir,Sanya Shabbir,Fozia Raza,Nasir Uddin,Nasir Uddin,Nasir Uddin +10 more
TL;DR: Structural characteristics of molecular complex between human TMPRSS2 and SARS-CoV-2 spike protein are provided and points to the candidate drug targets that could further be exploited to direct structure base drug designing.
Journal ArticleDOI
Afatinib reverses multidrug resistance in ovarian cancer via dually inhibiting ATP binding cassette subfamily B member 1
Shengqi Wang,Shi-ting Liu,Boxin Zhao,Fuheng Yang,Ya-Tian Wang,Qianying Liang,Yabin Sun,Yuan Liu,Zhi-hua Song,Yun Cai,Guofeng Li +10 more
TL;DR: Combining afatinib with chemotherapeutic drugs in ovarian cancer can facilitate the rediscovery of superior MDR reversal agents from molecular targeted drugs to provide a more effective and safer way of resensitizing MDR.
Journal ArticleDOI
Modeling the binding of diverse ligands within the Ah receptor ligand binding domain.
TL;DR: Specific residues within the AhR binding cavity are predicted that play a critical role in binding of three distinct groups of chemicals, providing an avenue for understanding ligand modulation of the Ahr functionality and for rational drug design.
Journal ArticleDOI
Plant phenolic volatiles inhibit quorum sensing in pectobacteria and reduce their virulence by potential binding to ExpI and ExpR proteins.
Janak Raj Joshi,Janak Raj Joshi,Netaly Khazanov,Hanoch Senderowitz,Saul Burdman,Alexander Lipsky,Iris Yedidia +6 more
TL;DR: In this article, volatile EOs, such as carvacrol and eugenol, were shown to specifically interfere with QS, the master regulator of virulence in pectobacteria, resulting in strong inhibition of QS genes, biofilm formation and PCWDEs.
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.