The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing.
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What is ProCheck?
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing.
How can I check stereochemistry of a protein structure?
Learn more. The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing.
What are global parameters of protein structure quality?
Global parameters include the distribution of phi, psi and chi 1 torsion angles, an … Stereochemical quality of protein structure coordinates Proteins. 1992 Apr;12(4):345-64.doi: 10.1002/prot.340120407.
What is a systematic technique for protein modelling?
A systematic technique for protein modelling that is applicable to the design of drugs, peptide vaccines and novel proteins is described. Our approach is knowledge-based, depending on the structures of homologous or analogous proteins and more generally on a relational data base of protein three-dimensional structures.
What does PROCHECK do?
PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
How do you run Procheck?
It takes a while to run, so be patient, and pray your browser doesn't time out....To run PROCHECK:Enter the 4-letter PDB code of the protein of interest, its chain ID (if required) and its resolution.Click on RUN to run the program.Click on Reset to enter new code.
How do you analyze protein structure?
The main technique that has been used to discover the three-dimensional structure of molecules, including proteins, at atomic resolution is x-ray crystallography.
What is verify3d?
Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures.
What does a Ramachandran plot show?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
How do you use Modrefiner?
Cut and paste the structure you want to refine (C-alpha trace, main-chain model or full-atomic model) in PDB format here: Or upload the target structure file from your local computer: Upload a reference structure (only C-alpha trace required) to which the refined model will be driven (Optional):
Which software is used for protein structure analysis?
MODELLER. MODELLER is a computer program for comparative protein structure modeling (http://salilab.org/modeller) (17,18).
What are the 3 analytical methods for determining protein content?
There are three major protein analysis techniques: protein separation, western blotting and protein identification.
Can PyMol predict protein structure?
The 3D structure of any protein sequence can be predicted by PyMol (http://www.pymol.org/), UCSF Chimera (http://www.rbvi.ucsf.edu/chimera/) and Antheprot 3D (https://www.antheprot-pbil.ibcp.fr) by inputting the PDB file of the polypeptide sequence. Hope it helps!
What is Errat score?
ERRAT is a so-called “overall quality factor” for non-bonded atomic interactions, with higher scores indicating higher quality. The generally accepted range is >50 for a high quality model. For the current 3D model, the overall quality factor predicted by the ERRAT server was 80.524 (Figure 3).
What is Q mean score?
QMEAN is a composite scoring function which is able to derive both global (i.e. for the entire structure) and local (i.e. per residue) absolute quality estimates on the basis of one single model. There are two global score values, QMEAN4 and QMEAN6. QMEAN4 is a linear combination of four statistical potential terms.
How do you cite Pdbsum?
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows
What is a procheck?
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive residue-by-residue listing. These give an assessment of the overall quality of the structure as compared with well refined structures of the same resolution and also highlight regions that may need further investigation. The PROCHECK programs are useful for assessing the quality not only of protein structures in the process of being solved but also of existing structures and of those being modelled on known structures.
What is the target of the spike protein?
One of the most important pieces of this host-pathogen interaction is the spike protein, which binds to the human Angiotensin-converting enzyme 2 (hACE2) cell receptor, mediates the membrane fusion and is the major target of neutralizing antibodies against SARS-CoV-2.
What is the PostScript language?
The PostScript Language Reference Manual, contains the complete semantics of every PostScript language operator, the Display PostScript System, PostScript Level 1 (the original PostScript language), and PostScript Level 2, the first major revision to the language since its release in 1985.
What is the function of the RNA transcription complex?
The RNA transcription complex (RTC) from the virus, SARS-CoV-2, is responsible for recognizing and processing RNA for two principal purposes. The RTC copies viral RNA for propagation into new virus and for ribosomal transcription of viral proteins. To accomplish these activities the RTC mechanism must also conform to a large number of imperatives including RNA over DNA base recognition, base pairing, distinguishing viral and host RNA, production of mRNA that conforms to host ribosome conventions, interface with error checking machinery and evading host immune responses. In addition, the RTC will discontinuously transcribe specific sections of viral RNA to amplify certain proteins over others. Central to SARS-CoV-2 viability, the RTC is therefore dynamic and sophisticated. We have conducted a systematic structural investigation of three components that make up the RTC: Nsp7, Nsp8 and Nsp12 (also known as RNA dependent RNA polymerase (RdRp)). We have solved high resolution crystal structures of the Nsp7/8 complex providing insight into the interaction between the proteins. We have used small angle X-ray and neutron solution scattering (SAXS and SANS) on each component individually as pairs and higher order complexes and with and without RNA. Using size exclusion chromatography and multi-angle light scattering coupled SAXS (SEC-MALS-SAXS) we defined which combination of components form transient or stable complexes. We used contrast matching neutron scattering to mask specific complex forming components to test whether components change conformation upon complexation. Altogether, we find that individual Nsp7, Nsp8 and Nsp12 structures vary based on whether other proteins in their complex are present. Combining our crystal structure, atomic coordinates reported elsewhere, SAXS, SANS and other biophysical techniques we provide greater insight into the RTC assembly, mechanism and potential avenues for disruption of the complex and its functions.
What is the role of ClpC1 in TB?
Due to increased cases of drug resistance to Mtb , a new treatment regime for TB needs to be discovered. ClpC1 plays a crucial role in the protein homeostasis of Mtb thus, presents as a promising target in controlling TB infection. The present study aimed to identify potential inhibitors for the ClpC1 N-terminal domain (ClpC1-NTD) by applying the relaxed complex scheme in virtual screening that accounts for the target and ligand flexibility. A filtered library of natural product compounds was virtually screened against each of the selected ClpC1-NTD dominant conformations from the ensemble generated using molecular dynamics simulation. The promising compounds with the strong binding affinity to ClpC1 protein were then further analysed for their molecular interactions. The stability of the most potent compound was examined through a complex MD simulation while the pharmacokinetics properties were gathered using SwissADME and pkCSM. The results showed that ligand NP132 formed a strong and stable complex with good pharmacokinetics and toxicological profile.
Is streptomycin a first line antibiotic?
The major challenge for controlling this infectious disease is the emergence and spread of drug-resistant Mycobacterium tuberculosis, the causative agent of TB. The antibiotic streptomycin is not a current first-line anti-TB drug. However, WHO recommends its use in patients infected with a streptomycin-sensitive strain. Several mutations in the M. tuberculosisrpsL, rrs and gidB genes have proved association with streptomycin resistance. In this study, we performed a molecular analysis of these genes in clinical isolates to determine the prevalence of known or novel mutations. Here, we describe the genetic analysis outcome. Furthermore, a biocomputational analysis of the MtGidB L101F variant, the product of a novel mutation detected in gidB during molecular analysis, is also reported as a theoretical approach to study the apparent genotype-phenotype association.