Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
3,888
result(s) for
"Rose, Peter"
Sort by:
Impact of genetic variation on three dimensional structure and function of proteins
The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.
Journal Article
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
[...]the notebook is made available, along with its data (Rule 8), in a manner encouraging public exploration and contribution (Rules 9–10). https://doi.org/10.1371/journal.pcbi.1007007.g001 Rule 1: Document the process, not just the results Computational notebooks’ interactivity makes it quick and easy to try out and compare different approaches or parameters—so quick and easy that we often fail to document those interactive investigations at the time we perform them. [...]the advice long provided regarding paper lab scientific notebooks becomes even more critical: make sure to document all your explorations, even (or perhaps especially) those that led to dead ends. Version control systems compare differences in these JSON files, not differences in the user-friendly notebook graphical user interface (GUI). Because of this, reported differences between versions of a given notebook are usually difficult for users to find and understand because they are expressed as changes in the abstruse JSON metadata for the notebook. Perform preparatory steps, like data cleaning, directly in the notebook and avoid manual interventions. Because notebooks’ interactivity make them vulnerable to accidental overwriting or deletion of critical steps by the user, if your analysis runs quickly, make a habit of regularly restarting your kernel and rerunning all cells to make sure you did not accidentally delete a step while cleaning your notebook (and if you did, retrieve the code for it from version control).
Journal Article
MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures
Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.
Journal Article
Separating single- from multi-particle dynamics in nonlinear spectroscopy
Quantum states depend on the coordinates of all their constituent particles, with essential multi-particle correlations. Time-resolved laser spectroscopy
1
is widely used to probe the energies and dynamics of excited particles and quasiparticles such as electrons and holes
2
,
3
, excitons
4
–
6
, plasmons
7
, polaritons
8
or phonons
9
. However, nonlinear signals from single- and multiple-particle excitations are all present simultaneously and cannot be disentangled without a priori knowledge of the system
4
,
10
. Here, we show that transient absorption—the most commonly used nonlinear spectroscopy—with
N
prescribed excitation intensities allows separation of the dynamics into
N
increasingly nonlinear contributions; in systems well-described by discrete excitations, these
N
contributions systematically report on zero to
N
excitations. We obtain clean single-particle dynamics even at high excitation intensities and can systematically increase the number of interacting particles, infer their interaction energies and reconstruct their dynamics, which are not measurable via conventional means. We extract single- and multiple-exciton dynamics in squaraine polymers
11
,
12
and, contrary to common assumption
6
,
13
, we find that the excitons, on average, meet several times before annihilating. This surprising ability of excitons to survive encounters is important for efficient organic photovoltaics
14
,
15
. As we demonstrate on five diverse systems, our procedure is general, independent of the measured system or type of observed (quasi)particle and straightforward to implement. We envision future applicability in the probing of (quasi)particle interactions in such diverse areas as plasmonics
7
, Auger recombination
2
and exciton correlations in quantum dots
5
,
16
,
17
, singlet fission
18
, exciton interactions in two-dimensional materials
19
and in molecules
20
,
21
, carrier multiplication
22
, multiphonon scattering
9
or polariton–polariton interaction
8
.
Transient absorption with
N
prescribed excitation intensities allows isolation of
N
increasingly nonlinear responses, enabling separation of single- and multiple-exciton dynamics.
Journal Article
مليحة : التاريخ غير المدون
يتناول كتاب (مليحة : التاريخ غير المدون) والذي قام بتأليفه (صباح عبود جاسم) في حوالي (141) صفحة من القطع المتوسط موضوع (آثار الشارقة في الإمارات العربية المتحدة)) مستعرضا المحتويات التالية : مقدمة بقلم صباح عبود جاسم، مدخل، فترة العصر الحجري القديم، فترة العصر الحجري الحديث، العصر البرونزي، العصر الحديدي : نظام الفلج والجمل العربي، فترة ما قبل الإسلام ومدينة مليحة، الجمل والحصان.
Book
Towards an efficient compression of 3D coordinates of macromolecular structures
The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.
Journal Article