A5084490031- Enzyme Structure and Function
- Protein Structure and Dynamics
- Photosynthetic Processes and Mechanisms
- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Advanced Electron Microscopy Techniques and Applications
- Computational Drug Discovery Methods
- Machine Learning in Materials Science
- Crystallography and molecular interactions
- Mass Spectrometry Techniques and Applications
- RNA and protein synthesis mechanisms
- X-ray Diffraction in Crystallography
- Carbohydrate Chemistry and Synthesis
- Advanced Combustion Engine Technologies
- Biochemical and Molecular Research
- Photoreceptor and optogenetics research
- Glycosylation and Glycoproteins Research
- SARS-CoV-2 and COVID-19 Research
- Peptidase Inhibition and Analysis
- Electron and X-Ray Spectroscopy Techniques
- Combustion and flame dynamics
- Microbial Metabolic Engineering and Bioproduction
- Advanced Thermodynamics and Statistical Mechanics
- Radioactive element chemistry and processing
- Free Radicals and Antioxidants
Lawrence Berkeley National Laboratory
2016-2025
University of California, Berkeley
1997-2023
Oncode Institute
2023
The Netherlands Cancer Institute
2023
Elucid Bioimaging
2019
Berkeley College
2015
CIC bioGUNE
2011
Australian Defence Force Academy
1996
UNSW Sydney
1993-1996
Lund University
1996
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...
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...
phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with wide range of upper resolution limits using large repertoire model parameterizations. It has several automation features and also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined strategies can be applied to specific parts in single run. An intuitive graphical user interface available...
Structural genomics seeks to expand rapidly the number of protein structures in order extract maximum amount information from genomic sequence databases. The advent several large-scale projects worldwide leads many new challenges field crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This will provide necessary algorithms proceed reduced intensity...
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...
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE statistical phenix.refine refinement. Recent advances in the include detection application of NCS from models as they are built, extensive model-completion algorithms solvent-molecule picking. Model-completion loop crossovers between chains different side-chain optimization. has been applied to set 48 structures at resolutions ranging 1.1 3.2 A,...
The electronic Ligand Builder and Optimization Workbench (eLBOW) is a program module of the PHENIX suite computational crystallographic software. It designed to be flexible procedure that uses simple fast quantum-chemical techniques provide chemically accurate information for novel known ligands alike. A variety input formats options allow attainment number diverse goals including geometry optimization generation restraints.
Estimates of the quality experimental maps are important in many stages structure determination macromolecules. Map is defined here as correlation between a map and corresponding obtained using phases from final refined model. Here, ten different measures were examined set 1359 calculated by re-analysis 246 solved MAD, SAD MIR data sets. A simple Bayesian approach to estimation one or more presented. It was found that estimator based on skewness density values an electron-density most...
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted a rapidly increasing number atomic models biomacromolecules that been solved using this technique and deposited Protein Data Bank Electron Microscopy Bank. Similar to macromolecular crystallography, validation tools for these maps are required. While some may be borrowed from new methods specifically designed cryo-EM Here, computational implemented PHENIX discussed, including d
The crystallographic maps that are routinely used during the structure-solution workflow almost always model-biased because model information is for their calculation. As these also to validate atomic models result from building and refinement, this constitutes an immediate problem: anything added will manifest itself in map thus hinder validation. OMIT a common tool verify presence of atoms model. simplest way compute exclude question structure, update corresponding structure factors...
Approximately 85% of the structures deposited in Protein Data Bank have been solved using X-ray crystallography, making it leading method for three-dimensional structure determination macromolecules. One limitations is that typical data quality (resolution) does not allow direct H-atom positions. Most hydrogen positions can be inferred from other atoms and therefore readily included into model as a priori knowledge. However, this may case biologically active sites macromolecules, where...
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.
In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported room-temperature structures PS four (semi)stable S-states, S
Abstract Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires transport two molecules and four protons from OEC. A high-resolution 1.89 Å structure obtained averaging all S states refining data various time points during 2 3 transition has provided better visualization potential pathways for substrate insertion proton release. Our results indicate that O1 channel...
Abstract In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms first step solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where Mn 4 CaO 5 cluster stores four oxidizing equivalents, S 0 to intermediate states Kok cycle, sequentially generated by photochemical charge separations center then catalyzes O–O bond formation chemistry 1–3 . Here, we report room temperature snapshots serial...
Abstract Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 essential for viral replication. In addition, PLpro dysregulates the host immune response cleaving ubiquitin and interferon-stimulated gene 15 protein proteins. As a result, promising target inhibition small-molecule therapeutics. Here we design series...
A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed the automation of crystallographic structure solution.This will provide necessary algorithms to proceed from reduced intensity data a refined molecular model, and facilitate solution both novice expert crystallographer.Here we review features briefly describe recent advances in infrastructure algorithms.
The advent of structural genomics initiatives has led to a pressing need for high-throughput macromolecular structure determination. To accomplish this, new methods and inevitably software must be developed accelerate the process solution. minimize duplication effort generate maintainable code efficiently, toolbox basic crystallographic components is required. development Computational Crystallography Toolbox ( cctbx ) been undertaken this purpose. In paper, fundamental requirements are...