MolProbity: More and better reference data for improved all‐atom structure validation
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Summary
Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by Mol probity's unique all‐atom clashscore.
- Type
- article
- Published
- 2018-01-01
- Cited by
- 4,138
- References
- 82
- Access
- Open access
- OpenAlex
- https://openalex.org/W2765322245
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3295839
Keywords
Python (programming language), Computer science, Software, Source code, Open source
References
- NGL Viewer: a web application for molecular visualization
- Using C-Alpha Geometry to Describe Protein Secondary Structure and Motifs
- Atoms in molecules
- Computational Methods for RNA Structure Validation and Improvement.
- Recommendations of the wwPDB NMR Validation Task Force
- PROCHECK: a program to check the stereochemical quality of protein structures
- Erratum: Representations of molecular force fields. V. On the equilibrium structure of methane
- Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
- Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
- Determination of Relative N−HN, N−C‘, Cα−C‘, and Cα−Hα Effective Bond Lengths in a Protein by NMR in a Dilute Liquid Crystalline Phase
- Correcting pervasive errors in RNA crystallography through enumerative structure prediction
- A systematic pairwise comparison of geometric parameters obtained by X-ray and neutron diffraction
- Calculation of the crystal structures of hydrocarbons by molecular packing analysis
- The structure of a plant photosystem I supercomplex at 3.4 Å resolution
- Implementing an X-ray validation pipeline for the Protein Data Bank
- Conformation Dependence of Backbone Geometry in Proteins
- van der Waals Volumes and Radii
- The Cambridge Structural Database: a quarter of a million crystal structures and rising.
- Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
- Coherent X‐Ray Scattering for the Hydrogen Atom in the Hydrogen Molecule
Cited by
- Regioselectivity of hyoscyamine 6β-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations
- Exploring CCRL2 chemerin binding using accelerated molecular dynamics
- Nucleic Acid Mediated Activation of a Short Prokaryotic Argonaute Immune System
- Real-space refinement in PHENIX for cryo-EM and crystallography
- Drosophila melanogaster Guk-holder interacts with the Scribbled PDZ1 domain and regulates epithelial development with Scribbled and Discs Large
- Cryo-EM visualization of an active high open probability CFTR ion channel
- Cryo-EM structure of the polycystin 2-l1 ion channel
- Synthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo[1,2-a]pyrimidines
- Investigation of structure and function of mitochondrial alcohol dehydrogenase isozyme III from Komagataella phaffii GS115.
- An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains
- The crystal structure and oligomeric form of Escherichia colil,d-carboxypeptidase A.
- Membrane insertion of α-xenorhabdolysin in near-atomic detail
- Insight into vitamin B6‐dependent epilepsy due to PLPBP (previously PROSC) missense mutations
- Discovery of a novel stereospecific β-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis
- CryoEM structures of complex I from mouse heart mitochondria in two biochemically-defined states
- Orthosteric and allosteric action of the C5a receptor antagonists
- Structure of the μ Opioid Receptor-Gi Protein Complex
- Structural Biology Helps Interpret Variants of Uncertain Significance in Genes Causing Endocrine and Metabolic Disorders
- Docking techniques in pharmacology: How much promising?
- The first transmembrane region of complement component-9 acts as a brake on its self-assembly
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