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
In vitro and in silico antifungal efficacy of nitrogen-doped carbon nanohorn (NCNH) against Rhizoctonia solani.
Seema Dharni,Sanchita,Sreekuttan M. Unni,Sreekumar Kurungot,Abdul Samad,Ashok Sharma,Dharani Dhar Patra +6 more
TL;DR: In vitro antifungal efficiency of nitrogen-doped carbon nanohorn against Rhizoctonia solani showed that growth of fungi in the presence of NCNH was significantly inhibited at 150 μg mL−1 after 72 h, which is the first report of antIfungal efficacy ofNCNH against R. solani.
Journal ArticleDOI
Molecular and structural insights into FaEXPA5, an alpha-expansin protein related with cell wall disassembly during ripening of strawberry fruit
TL;DR: The full length of this α-expansin (FaEXPA5), whose had been related with fruit softening, is reported and the protein structural was described by homology model, and MD simulations showed that FaEXPA 5 can interact with the ligands through residues present in the open groove along the two domains.
Journal ArticleDOI
Molecular docking and molecular dynamics study on SmHDAC1 to identify potential lead compounds against Schistosomiasis
TL;DR: Light is thrown on the reliable model for further structure based drug designing, concerning SmHDAC1 of S. mansoni, and 24th inhibitor (N,8-dihydroxy-8-(naphthalen-2-yl) octanamide zinc id- ZINC13474421) showed better binding with SmHDac1 as compared to Hs HDAC1 in terms of binding energy and supported by IC50 value.
Journal ArticleDOI
Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays.
Magambo Phillip Kimuda,Magambo Phillip Kimuda,Dustin Laming,Heinrich C. Hoppe,Özlem Tastan Bishop +4 more
TL;DR: Five compounds which showed low micromolar Trypanosome growth inhibition in in vitro experiments that might be acting by inhibition of TbPTR1 are identified and provide a basis for scaffold optimization for further studies in the development of HAT anti-folates.
Journal ArticleDOI
In Silico Insight into the Dominant Type II Toxin–Antitoxin Systems and Clp Proteases in Listeria monocytogenes and Designation of Derived Peptides as a Novel Approach to Interfere with this System
TL;DR: This study used several valid servers to predict the protein models of three TA complexes and their regulatory Clp proteases in L. monocytogenes as well as their associated interactions following docking result analysis to determine potential inhibitory peptides that would act as TA inhibitors paving the way for novel therapeutic developments to combat listeriosis infection.
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.