A5003066498- Enzyme Structure and Function
- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
- Mass Spectrometry Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Methane Hydrates and Related Phenomena
- Advanced Data Processing Techniques
- Advanced Electron Microscopy Techniques and Applications
- Advanced Data Storage Technologies
- Analytical Chemistry and Chromatography
- Computational Drug Discovery Methods
- Radioactive element chemistry and processing
- Advanced NMR Techniques and Applications
Institut de Biologia Molecular de Barcelona
2020-2024
The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with mission to develop, test, distribute and promote software for macromolecular crystallography. CCP suite multiplatform collection of programs brought together by familiar execution routines, set common libraries graphical interfaces. has experienced several considerable changes since its last reference article, involving new infrastructure, original This which intended as general literature citation...
Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at cost increasing data volumes. This due to deployment modern high-speed, high-resolution detectors, increased complexity and variety crystallographic software, use extensive databases high-performance computing. limits what can be accomplished with personal, offline, computing equipment terms both productivity maintainability. There also an issue long-term...
is a lightweight graphical user interface (GUI) for the
Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in that present large differences due to relative movement domains or poorly predicted areas, very accurate regions tend be present. These are successful fragment-based phasing as implemented ARCIMBOLDO. The particularities inherently addressed new predicted_model mode, rendering preliminary treatment superfluous but also...
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility essential in order capture small local differences. ALEPH software optimized for the extraction protein folds by relying on their geometry rather than sequence. annotation variability a given fold provides valuable information fragment-based...
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using common secondary-structure or tertiary-structure template library of folds, locates these with Phaser and reveals the rest by density modification autotracing in SHELXE. The latter stage is challenging when dealing diffraction data at lower resolution, low solvent content, high β-sheet composition situations which initial fragments represent fraction total scattering where...
Abstract Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in absence of a model. In addition, bias more severe when independent data are scarce. Our methods solve phase problem by combining location accurate fragments using Phaser with density modification and interpretation resulting maps SHELXE. From partial, correct structure, process stereochemical constraints draw rest validating result. This same principle now...
RCIMBOLDO [1] is a fragment based molecular replacement framework where Local Folds (LF: small discontinuous fragments) are located with PHASER [2] providing phases that improved and interpreted in SHELXE [3].ALEPH [4] program for retrieving structural properties of proteins from the PDB [5], solely on geometrical descriptors, Characteristic Vectors (CVs) [6], computed as centroid C -O vectors consecutive tripeptides.Networks CVs hold angles distances representing protein structure. ALEPH...
The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility essential in order capture small local differences. ALEPH software optimized for the extraction protein folds by relying on their geometry rather than sequence. annotation variability a given fold provides valuable information fragment-based...
Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using common secondary-structure or tertiary-structure template library of folds, locates these with Phaser and reveals the rest by density modification autotracing in SHELXE. The latter stage is challenging when dealing diffraction data at lower resolution, low solvent content, high β-sheet composition situations which initial fragments represent fraction total scattering where...