A5038747965- Protein Structure and Dynamics
- Genomics and Chromatin Dynamics
- Black Holes and Theoretical Physics
- Advanced NMR Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- NMR spectroscopy and applications
- Advanced Fluorescence Microscopy Techniques
- Genomics and Phylogenetic Studies
- Cosmology and Gravitation Theories
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Computational Physics and Python Applications
- Metabolomics and Mass Spectrometry Studies
- Genetic diversity and population structure
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Advanced MRI Techniques and Applications
- CRISPR and Genetic Engineering
- Noncommutative and Quantum Gravity Theories
- Distributed and Parallel Computing Systems
- Ubiquitin and proteasome pathways
- Advanced Biosensing Techniques and Applications
- Bioinformatics and Genomic Networks
- Single-cell and spatial transcriptomics
- Monoclonal and Polyclonal Antibodies Research
University of Cambridge
2011-2024
Dulbecco Telethon Institute
2011
Wilmington University
1993
Fermi National Accelerator Laboratory
1988
University of Chicago
1986-1988
Abstract To address data management and exchange problems in the nuclear magnetic resonance (NMR) community, Collaborative Computing Project for NMR community (CCPN) created a “Data Model” that describes all different types of information needed an structural study, from molecular structure parameters to coordinates. This paper development set software applications use Data Model its associated libraries, thus validating approach. These are freely available provide pipeline high‐throughput...
NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both structural- and functional studies. However, in practice complexity has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, latest software release from Collaborative Computational Project NMR, all aspects data analysis, including liquid- solid-state data. This been designed to be simple, flexible, aims ensure that routine tasks...
We investigate theories in which classical and quantum-mechanical degrees of freedom interact dynamically. In commonly used semiclassical theories, such as those to study inflationary-universe models, quantum fluctuations do not affect the dynamics variables. construct a new theory each other; Wigner probability function turns out be special case. Relevance calculations perturbations from inflation are discussed.
Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies protein structure, function and dynamics. Software development, however, not kept pace with these advances data analysis is mostly performed using tools developed for solution which do directly address solid-state specific issues. Here we present additions to the CcpNmr Analysis software package enable easier identification spinning side...
It is shown that anti---de Sitter spacetime the unique solution to ${R}_{\mathrm{ab}}=\ensuremath{\Lambda}{g}_{\mathrm{ab}}$ with $\ensuremath{\Lambda}<0$ which strictly stationary and asymptotically Sitter. Thus, in absence of horizons, there are no soliton solutions Einstein's equation negative cosmological constant. The analogous statement for de ($\ensuremath{\Lambda}>0$) discussed some preliminary results obtained.
Recent developments in in-cell NMR techniques have allowed us to study proteins detail inside living eukaryotic cells. In order complement the existing protocols, and extend range of possible applications, we introduce a novel approach for observing spectra using sf9 cell/baculovirus system. High-resolution 2D (1)H-(15)N correlation were observed four model expressed Furthermore, 3D triple-resonance Streptococcus protein G B1 domain cells by nonlinear sampling overcome short lifetime samples...
CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make such pivotal technique research into complex questions. This report describes how can seamlessly link together all tasks in structure-determination process. It details each stages from generating restraints [distance, dihedral, hydrogen bonds residual dipolar...
Abstract To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers enhancer–promoter interactions, we have developed an approach to segment extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds chromatin for minutes, decompacts structure increases enhancer dynamics. We also uncovered a rare fast-diffusing state of found restricts time spent in state. Hi-C...
Enhancers bind transcription factors, chromatin regulators, and non-coding transcripts to modulate the expression of target genes. Here, we report 3D genome structures single mouse ES cells as they are induced exit pluripotency transition through a formative stage prior undergoing neuroectodermal differentiation. We find that there is remarkable reorganization structure where inter-chromosomal intermingling increases dramatically in state. This associated with formation large number multiway...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFour-dimensional heteronuclear triple resonance NMR methods for the assignment of backbone nuclei in proteinsWayne Boucher, Ernest D. Laue, Sharon Campbell-Burk, and Peter J. DomailleCite this: Am. Chem. Soc. 1992, 114, 6, 2262–2264Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://pubs.acs.org/doi/10.1021/ja00032a053https://doi.org/10.1021/ja00032a053research-articleACS...
A major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods time dense environments found living cells. Here, we introduce concept using FRET to enhance photophysical properties photo-modulatable (PM) fluorophores commonly used such studies. By developing novel pairs, consisting a PM donor fluorophore (either mEos3.2 PA-JF549) next photostable acceptor dye JF646, demonstrate that competes with normal photobleaching kinetic pathways increase...
Motivation: The lack of standards for storage and exchange data is a serious hindrance the large-scale deposition, mining program interoperability that becoming increasingly important in bioinformatics. problem lies not only defining maintaining standards, but also convincing scientists application programmers with wide variety backgrounds interests to adhere them.
Stem cell differentiation involves major chromatin reorganisation, heterochromatin formation and genomic relocalisation of structural proteins, including protein 1 gamma (HP1γ). As the principal reader repressive histone marks H3K9me2/3, HP1 plays a key role in numerous processes maintenance. We find that HP1γ is citrullinated mouse embryonic stem cells (mESCs) this diminishes when differentiate, indicating it dynamically regulated post-translational modification during differentiation....
We present here the freely available Metabolomics Project resource specifically designed to work under CcpNmr Analysis program produced by CCPN (Collaborative Computing for NMR) (Vranken et al., 2005, The data model NMR spectroscopy: development of a software pipeline. Proteins, 59, 687-696). project consists database assigned 1D and 2D spectra many common metabolites. aims help user analyze assign unknown metabolite mixtures. Spectra mixtures can be easily superimposed compared with...
Data management has emerged as one of the central issues in high-throughput processes taking a protein target sequence through to sample. To simplify this task, and following extensive consultation with international structural genomics community, we describe here model data related production. The is suitable for both large small facilities use tracking samples, experiments, results many procedures involved. described Unified Modeling Language (UML). In addition, present relational database...