A5035236781- Colonialism, slavery, and trade
- Enzyme Structure and Function
- Protein Structure and Dynamics
- Historical Economic and Social Studies
- RNA and protein synthesis mechanisms
- Global Maritime and Colonial Histories
- Glycosylation and Glycoproteins Research
- Protein purification and stability
- Advanced Proteomics Techniques and Applications
- Metal-Catalyzed Oxygenation Mechanisms
- Caribbean history, culture, and politics
- African history and culture studies
- Computational Drug Discovery Methods
- Race, History, and American Society
- Peptidase Inhibition and Analysis
- Genetics, Bioinformatics, and Biomedical Research
- Cuban History and Society
- Enzyme Production and Characterization
- Culture, Economy, and Development Studies
- Biochemical and Molecular Research
- Advanced Electron Microscopy Techniques and Applications
- Chemical Synthesis and Analysis
- Mass Spectrometry Techniques and Applications
- Hemoglobin structure and function
- Historical Studies and Socio-cultural Analysis
Duke University
2012-2025
Duke University Hospital
2009-2023
Duke Medical Center
2009-2023
Stellenbosch University
2022
University of Hull
2008-2021
Yale University
2017
University of Reading
2015
University of Canberra
2013
Sheffield Hallam University
2009
Wilberforce University
2008
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required solve complete many of these structures because the need for manual interpretation complex numerical data using software packages repeated use interactive three-dimensional graphics. PHENIX has been developed provide comprehensive system macromolecular crystallographic structure solution with an emphasis on automation all...
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for proteins nucleic acids. It relies heavily on power sensitivity provided by optimized hydrogen placement all-atom contact analysis, complemented updated versions covalent-geometry torsion-angle criteria. Some corrections can be performed automatically in all diagnostics are presented chart graphical forms help guide manual rebuilding....
Diffraction (X-ray, neutron and electron) electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which required understand biological processes develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of reduced experimental data different. Software tools structure determination should therefore be tailored each method. Phenix a comprehensive...
Abstract Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot. Deviation of observed atom from ideal position provides single encapsulating major structure‐validation information contained in bond angle distortions. deviation sensitive to incompatibilities between sidechain backbone caused by misfit conformations or inappropriate refinement restraints. A ϕ,ψ plot using density‐dependent smoothing for 81,234 non‐Gly, non‐Pro, non‐prePro...
Abstract This paper describes the current update on macromolecular model validation services that are provided at MolProbity website, emphasizing changes and additions since previous review in 2010. There have been many infrastructure improvements, including rewrite of Java utilities to now use existing or newly written Python open‐source CCTBX portion Phenix software system. improves long‐term maintainability enhances thorough integration MolProbity‐style within Phenix. is a complete mirror...
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis any steric problems within the molecules as well updated dihedral-angle diagnostics, it can calculate display H-bond van der Waals contacts in interfaces between components. An integral step process addition full optimization all hydrogen atoms, both polar nonpolar. New functions have been added RNA, interfaces, NMR...
A definition based on α-carbon positions and a sample of 215 α helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual relative the helix ends. The interface residue, which is half in out helix, called N-cap or C-cap, whichever appropriate. results confirm earlier observations, such as asymmetrical charge distributions first last helical turn, but several new, sharp are found well. most striking these 3.5:1 preference Asn at...
MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis any steric problems within the molecules can calculate display H-bond van der Waals contacts in interfaces between components. An integral step process addition full optimization all hydrogen atoms, both polar nonpolar. The results are reported multiple forms: as overall numeric scores, lists,...
All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those B-factors >/=40 or van der Waals >/=0.4 A) greatly improves the clustering populations. Asn, Gln, His side chains additionally benefit from flipping their planar terminal groups when required by H-bonding. Sensitivity to skew and boundaries chi angle bins is avoided using modes rather than...
The fact that natural β-sheet proteins are usually soluble but fragments or designs of β structure aggregate suggests must somehow be designed to avoid this problem. Regular edges dangerous, because they already in the right conformation interact with any other strand encounter. We surveyed edge strands a large sample all-β tabulate features could protect against further interactions. β-barrels, course, altogether by continuous H-bonding around barrel cylinder. Parallel β-helix their ends...
An electron density map at 3 angstrom resolution has been calculated for Cu2+, Zn2+ superoxide dismutase from bovine erythrocytes, and the course of main chain traced. The dominant structural feature is an 8-stranded barrel antiparallel beta-pleated sheet. There one very short helical section two long loops non-repetitive structure. Cu Zn are bound between side beta about 6 Angstrom apart, with a common histidine ligand. four ligands in somewhat distorted square plane, three histidines...
The protein Felix was designed de novo to fold into an antiparallel four-helix bundle of specific topology. Its sequence 79 amino acid residues is not homologous any known sequence, but "native-like" in that it nonrepetitive and contains 19 the 20 naturally occurring acids. has been expressed from a synthetic gene cloned Escherichia coli , purified homogeneity. Physical characterization indicates (i) monomeric solution, (ii) predominantly α-helical, (iii) intramolecular disulfide bond...
Simple models are presented that describe the rules for almost all packing occurs between and among alpha-helices pleated sheets. These rules, together with primary secondary structures, major determinants of three-dimensional structure proteins.
Two isomorphously substituted derivatives of the nuclease-Ca2+-thymidine 3',5'-diphosphate complex have been prepared and used in an x-ray crystallographic study molecular structure. In one case, 5-iododeoxyuridine was place thymidine (a net replacement CH3 by I), and, other, Ba2+ Ca2+. Intensities all reflections their Friedel pairs within 4 A sphere were measured on this inhibitor its two derivatives; addition, approximately 35% data between 2 collected, selection being made basis peak to...
Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran for improved macromolecular refinement phenix.refine at low resolution.
The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new features, and also describe how are fighting back against outside developments which compromise that mission. Our tool called UnDowser analyzes properties context of clashing HOH "waters" diagnose what they might actually represent; a dozen distinct scenarios illustrated described. We now treat alternate conformations more...