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MolProbity specifications


Unique identifier OMICS_04464
Name MolProbity
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline David C. Richardson

Publication for MolProbity

MolProbity citations


Targeting G protein coupled receptor signaling at the G protein level with a selective nanobody inhibitor

Nat Commun
PMCID: 5959942
PMID: 29777099
DOI: 10.1038/s41467-018-04432-0

[…] el adjustments with Coot 0.8.8. The final models had agreement factors Rfree and Rcryst of 24.7% and 20%, respectively. The stereochemical quality of the Gβ1γ1-Nb5 complex model was assessed with the Molprobity and wwPDB validation servers. Details of the diffraction data collection and structural refinement statistics are provided in Supplementary Table . Coordinates and structure factor amplitud […]


Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] 2 complex structure was determined by MR with PGV19 (determined in this study) and BG505 SOSIP.664+PGT122 from PDB 4TVP. The structures were refined using Phenix and model building performed in Coot. MolProbity, Privateer, and pdb-care were used for structure validation. The refinement statistics are reported in Supplementary Table . […]


Immune Informatic Analysis and Design of Peptide Vaccine From Multi epitopes Against Corynebacterium pseudotuberculosis

Bioinform Biol Insights
PMCID: 5954444
PMID: 29780242
DOI: 10.1177/1177932218755337

[…] accuracy of the global and local structure, as well as the physical correction in 59%, 67%, and 79% of the targets submitted to the refinement, using the parameters determined by GDT-HA, GDC-SC, and MolProbity score. After the refinement process, 5 models were provided, each presenting the parameters previously described. The first is made from smooth relaxation as the 4 additional models generat […]


Structural basis for the recognition of complex type N glycans by Endoglycosidase S

Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] e PHENIX suite. Model rebuilding was carried out with Buccaneer and the CCP4 suite. The final manual building was performed with Coot and refinement with phenix.refine. The structure was validated by MolProbity. Data collection and refinement statistics are presented in Supplementary Table . Atomic coordinates and structure factors have been deposited with the Protein Data Bank, accession code 6EN […]


Vaccine elicited receptor binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

Nat Commun
PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z
call_split See protocol

[…] tary Figure , and . Data collection and refinement statistics are listed in Supplementary Table . We used SBGrid-supported applications to complete our structural studies, validated structures using MolProbity, and made figures with the PyMol Molecular Graphics System, Schrödinger, LLC. […]


Structural and immunologic correlates of chemically stabilized HIV 1 envelope glycoproteins

PLoS Pathog
PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986
call_split See protocol

[…] ed in iterative centroid-representation density-guided rebuild-and-refinement in the Rosetta software suite []. Rosetta models were manually adjusted in Coot followed by evaluation based on geometry (MolProbity []) and cryo-EM density fit (EMRinger []). Upon convergence, the best model underwent iterative all-atom Rosetta refinement and manual rebuilding constrained by the cryo-EM density map and […]


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MolProbity institution(s)
Department of Biochemistry, Duke University, Durham, NC, USA

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