A5076793372- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Viral gastroenteritis research and epidemiology
- Bacillus and Francisella bacterial research
- Complex Network Analysis Techniques
- Animal Virus Infections Studies
- Opinion Dynamics and Social Influence
- Cosmology and Gravitation Theories
- Spectroscopy Techniques in Biomedical and Chemical Research
- Advanced Thermodynamics and Statistical Mechanics
- COVID-19 epidemiological studies
- Gamma-ray bursts and supernovae
- Microbial Metabolic Engineering and Bioproduction
- Pulsars and Gravitational Waves Research
- Vaccine Coverage and Hesitancy
- Complex Systems and Time Series Analysis
- Evolutionary Game Theory and Cooperation
- Biomedical Text Mining and Ontologies
- CRISPR and Genetic Engineering
- Origins and Evolution of Life
- Financial Markets and Investment Strategies
- Research on Leishmaniasis Studies
Constructor University
2017-2024
Constructing Excellence
2024
Baylor College of Medicine
2006-2017
Ajou University
2007
Max Planck Society
2000
Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...
Sewing Up DNA Repair All cells have a battery of DNA-repair pathways to help ensure genome maintenance and stability, including stress-induced break repair in Escherichia coli. Similar pathways—which can be mutagenic—are known yeast human the potential accelerate evolution. Sixteen proteins are required for pathway E. Al Mamun et al. (p. 1344 ) analyzed coli determine full complement protein contributions pathway. Ninety-three genes were found repair. One-third identified network involved...
Keeping up with the ever-expanding flow of data and publications is untenable poses a fundamental bottleneck to scientific progress. Current search technologies typically find many relevant documents, but they do not extract organize information content these documents or suggest new hypotheses based on this organized content. We present an initial case study KnIT, prototype system that mines contained in literature, represents it explicitly queriable network, then further reasons upon...
Abstract Background Structural genomics projects such as the Protein Structure Initiative (PSI) yield many new structures, but often these have no known molecular functions. One approach to recover this information is use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched other structures. Since experimentally determined sites are not common enough define on large scale, work tests...
Abstract Motivation: Predicting protein function is a central problem in bioinformatics, and many approaches use partially or fully automated methods based on various combination of sequence, structure other information proteins genes. Such establishes relationships between that can be modelled most naturally as edges graphs. A priori, however, it often unclear which from graph may contribute to accurate predictions. For reason, one established strategy integrate all available sources,...
We present KnIT, the Knowledge Integration Toolkit, a system for accelerating scientific discovery and predicting previously unknown protein-protein interactions. Such predictions enrich biological research are pertinent to drug understanding of disease. Unlike prior study, KnIT is now fully automated demonstrably scalable. It extracts information from literature, automatically identifying direct indirect references protein interactions, which knowledge that can be represented in network...
We investigate the possibility of a delayed detonation in Type Ia supernova under assumption that transition to is triggered by turbulence only. Our discussion based on Zeldovich mechanism and suggests typical turbulent velocities present during explosion are not strong enough allow this occur. Although we able show carbon-rich matter (e.g., X(12C) = 0.75) deflagration (DDT) enhanced, even case, needed larger than expected value u'(L) ≈ 107 cm s-1 length-scale L 106 cm. Thus conclude DDT may...
The development of new and effective drugs is strongly affected by the need to identify drug targets reduce side effects. Resolving these issues depends partially on a thorough understanding biological function proteins. Unfortunately, experimental determination protein expensive time consuming. To support accelerate functions, algorithms for prediction are designed gather evidence indicating functional similarity with well studied One such approach MASH pipeline, described in first half...
The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class computational solutions to this problem based on the similarity structure. Here, we implement simple yet efficient measure structure similarity, contact metric. Even though its computation avoids alignments and therefore nearly instantaneous, find that small values correlate with geometrical root mean square deviations obtained from alignments. To...
The annotation of protein function has not kept pace with the exponential growth raw sequence and structure data. An emerging solution to this problem is identify 3D motifs or templates in structures that are necessary sufficient determinants function. Here, we demonstrate recurrent use evolutionary trace information construct such for enzymes, search them other structures, distinguish true from spurious matches. Serine protease built evolutionarily important residues between proteases...
We present a statistical model which shows the influence of turbulence on thermonuclear flame propagating in C+O white dwarf matter. Based Monte Carlo description turbulence, it provides method for investigating physics so-called distributed burning regime. Using this method, we perform numerical simulations turbulent flames and show that particular regime flamelet velocity loses its validity. In fact, at high intensities, can lead to deceleration thus induce competing process effects cause...
Function prediction frequently relies on comparing genes or gene products to search for relevant similarities. Because the number of protein structures with unknown function is mushrooming, however, we asked here whether such comparisons could be improved by focusing narrowly key functional features structures, as defined Evolutionary Trace (ET). Therefore a series algorithms was built (a) extract local motifs (3D templates) from based ET ranking residue importance; (b) assess their...
From December 2019 to early March 2020, the local outbreak of novel corona virus disease (COVID-19) in central China's Hubei region has grown into a worldwide pandemic. This rapid and catastrophic escalation makes search for understanding underlying mechanisms infection disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well their associated risk factors an urgent priority. In particular, strong variations COVID-19 rates seen internationally require better...
High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and features in common; next, are linked together into a proteomic network of ETA similarities; then, starting from with functions, competing labels diffuse...
Abstract Background Annotating protein function with both high accuracy and sensitivity remains a major challenge in structural genomics. One proven computational strategy has been to group few key functional amino acids into templates search for these other structures, so as transfer when match is found. To this end, we previously developed Evolutionary Trace Annotation (ETA) showed that diffusing known annotations over network of template matches on genomic scale improved predictions...
In the human malaria parasite Plasmodium falciparum, membrane glutathione S-transferases (GST) have recently emerged as potential cellular detoxifying units and drug target candidates with artemisinin (ART) class of antimalarials inhibiting their activity at single-digit nanomolar potency when activated by iron sources such cytotoxic hematin. Here we put forward hypothesis that GST falciparum exported protein 1 (PfEXP1, PF3D7_1121600) might be directly involved in mode action unrelated...
The transmission of genomic information from coding sequence to protein structure during synthesis is subject stochastic errors. To analyze limits in the presence spurious errors, Shannon's noisy channel theorem applied a communication between amino acid sequences and their structures established large-scale statistical analysis atomic coordinates. While confirms that close native conformations transmitted with limited error probability, additional random errors (amino substitutions)...
<title>Abstract</title> SARS-CoV-2 spike (S) glycoprotein furin cleavage site is a key determinant of virulence and COVID-19 pathogencity. Located at the S1/S2 junction, it unique among sarbecoviruses but frequently found betacoronaviruses. Recent evidence suggests that this includes two additional functional motifs: pat7 nuclear localization signal flanking O-glycosites. However, systematic overview spikes bearing polyfunctional sequence domain has been missing. Here we report sequences...