8,374 research outputs found
Cooperative "folding transition" in the sequence space facilitates function-driven evolution of protein families
In the protein sequence space, natural proteins form clusters of families
which are characterized by their unique native folds whereas the great majority
of random polypeptides are neither clustered nor foldable to unique structures.
Since a given polypeptide can be either foldable or unfoldable, a kind of
"folding transition" is expected at the boundary of a protein family in the
sequence space. By Monte Carlo simulations of a statistical mechanical model of
protein sequence alignment that coherently incorporates both short-range and
long-range interactions as well as variable-length insertions to reproduce the
statistics of the multiple sequence alignment of a given protein family, we
demonstrate the existence of such transition between natural-like sequences and
random sequences in the sequence subspaces for 15 domain families of various
folds. The transition was found to be highly cooperative and two-state-like.
Furthermore, enforcing or suppressing consensus residues on a few of the
well-conserved sites enhanced or diminished, respectively, the natural-like
pattern formation over the entire sequence. In most families, the key sites
included ligand binding sites. These results suggest some selective pressure on
the key residues, such as ligand binding activity, may cooperatively facilitate
the emergence of a protein family during evolution. From a more practical
aspect, the present results highlight an essential role of long-range effects
in precisely defining protein families, which are absent in conventional
sequence models.Comment: 13 pages, 7 figures, 2 tables (a new subsection added
On the entropy of protein families
Proteins are essential components of living systems, capable of performing a
huge variety of tasks at the molecular level, such as recognition, signalling,
copy, transport, ... The protein sequences realizing a given function may
largely vary across organisms, giving rise to a protein family. Here, we
estimate the entropy of those families based on different approaches, including
Hidden Markov Models used for protein databases and inferred statistical models
reproducing the low-order (1-and 2-point) statistics of multi-sequence
alignments. We also compute the entropic cost, that is, the loss in entropy
resulting from a constraint acting on the protein, such as the fixation of one
particular amino-acid on a specific site, and relate this notion to the escape
probability of the HIV virus. The case of lattice proteins, for which the
entropy can be computed exactly, allows us to provide another illustration of
the concept of cost, due to the competition of different folds. The relevance
of the entropy in relation to directed evolution experiments is stressed.Comment: to appear in Journal of Statistical Physic
Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins.Fil: Parra, Rodrigo Gonzalo. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Espada, RocĂo. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Verstraete, Nina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Ferreiro, Diego Ulises. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Ciudad Universitaria. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de QuĂmica BiolĂłgica de la Facultad de Ciencias Exactas y Naturales; Argentin
NILM techniques for intelligent home energy management and ambient assisted living: a review
The ongoing deployment of smart meters and different commercial devices has made electricity disaggregation feasible in buildings and households, based on a single measure of the current and, sometimes, of the voltage. Energy disaggregation is intended to separate the total power consumption into specific appliance loads, which can be achieved by applying Non-Intrusive Load Monitoring (NILM) techniques with a minimum invasion of privacy. NILM techniques are becoming more and more widespread in recent years, as a consequence of the interest companies and consumers have in efficient energy consumption and management. This work presents a detailed review of NILM methods, focusing particularly on recent proposals and their applications, particularly in the areas of Home Energy Management Systems (HEMS) and Ambient Assisted Living (AAL), where the ability to determine the on/off status of certain devices can provide key information for making further decisions. As well as complementing previous reviews on the NILM field and providing a discussion of the applications of NILM in HEMS and AAL, this paper provides guidelines for future research in these topics.AgĂŞncia financiadora:
Programa Operacional Portugal 2020 and Programa Operacional Regional do Algarve
01/SAICT/2018/39578
Fundação para a Ciência e Tecnologia through IDMEC, under LAETA:
SFRH/BSAB/142998/2018
SFRH/BSAB/142997/2018
UID/EMS/50022/2019
Junta de Comunidades de Castilla-La-Mancha, Spain:
SBPLY/17/180501/000392
Spanish Ministry of Economy, Industry and Competitiveness (SOC-PLC project):
TEC2015-64835-C3-2-R MINECO/FEDERinfo:eu-repo/semantics/publishedVersio
On-premise containerized, light-weight software solutions for Biomedicine
Bioinformatics software systems are critical tools for analysing large-scale biological
data, but their design and implementation can be challenging due to the need for reliability, scalability, and performance. This thesis investigates the impact of several
software approaches on the design and implementation of bioinformatics software
systems. These approaches include software patterns, microservices, distributed
computing, containerisation and container orchestration. The research focuses on
understanding how these techniques affect bioinformatics software systems’ reliability, scalability, performance, and efficiency. Furthermore, this research highlights
the challenges and considerations involved in their implementation. This study also
examines potential solutions for implementing container orchestration in bioinformatics research teams with limited resources and the challenges of using container
orchestration. Additionally, the thesis considers microservices and distributed computing and how these can be optimised in the design and implementation process to
enhance the productivity and performance of bioinformatics software systems. The
research was conducted using a combination of software development, experimentation, and evaluation. The results show that implementing software patterns can
significantly improve the code accessibility and structure of bioinformatics software
systems. Specifically, microservices and containerisation also enhanced system reliability, scalability, and performance. Additionally, the study indicates that adopting
advanced software engineering practices, such as model-driven design and container
orchestration, can facilitate efficient and productive deployment and management of
bioinformatics software systems, even for researchers with limited resources. Overall, we develop a software system integrating all our findings. Our proposed system
demonstrated the ability to address challenges in bioinformatics. The thesis makes
several key contributions in addressing the research questions surrounding the design,
implementation, and optimisation of bioinformatics software systems using software
patterns, microservices, containerisation, and advanced software engineering principles and practices. Our findings suggest that incorporating these technologies can
significantly improve bioinformatics software systems’ reliability, scalability, performance, efficiency, and productivity.Bioinformatische Software-Systeme stellen bedeutende Werkzeuge für die Analyse
umfangreicher biologischer Daten dar. Ihre Entwicklung und Implementierung kann
jedoch aufgrund der erforderlichen Zuverlässigkeit, Skalierbarkeit und Leistungsfähigkeit eine Herausforderung darstellen. Das Ziel dieser Arbeit ist es, die Auswirkungen von Software-Mustern, Microservices, verteilten Systemen, Containerisierung
und Container-Orchestrierung auf die Architektur und Implementierung von bioinformatischen Software-Systemen zu untersuchen. Die Forschung konzentriert sich
darauf, zu verstehen, wie sich diese Techniken auf die Zuverlässigkeit, Skalierbarkeit,
Leistungsfähigkeit und Effizienz von bioinformatischen Software-Systemen auswirken
und welche Herausforderungen mit ihrer Konzeptualisierungen und Implementierung
verbunden sind. Diese Arbeit untersucht auch potenzielle Lösungen zur Implementierung von Container-Orchestrierung in bioinformatischen Forschungsteams mit begrenzten Ressourcen und die Einschränkungen bei deren Verwendung in diesem Kontext. Des Weiteren werden die Schlüsselfaktoren, die den Erfolg von bioinformatischen Software-Systemen mit Containerisierung, Microservices und verteiltem Computing beeinflussen, untersucht und wie diese im Design- und Implementierungsprozess optimiert werden können, um die Produktivität und Leistung bioinformatischer
Software-Systeme zu steigern. Die vorliegende Arbeit wurde mittels einer Kombination aus Software-Entwicklung, Experimenten und Evaluation durchgefĂĽhrt. Die
erzielten Ergebnisse zeigen, dass die Implementierung von Software-Mustern, die Zuverlässigkeit und Skalierbarkeit von bioinformatischen Software-Systemen erheblich
verbessern kann. Der Einsatz von Microservices und Containerisierung trug ebenfalls zur Steigerung der Zuverlässigkeit, Skalierbarkeit und Leistungsfähigkeit des
Systems bei. DarĂĽber hinaus legt die Arbeit dar, dass die Anwendung von SoftwareEngineering-Praktiken, wie modellgesteuertem Design und Container-Orchestrierung,
die effiziente und produktive Bereitstellung und Verwaltung von bioinformatischen
Software-Systemen erleichtern kann. Zudem löst die Implementierung dieses SoftwareSystems, Herausforderungen für Forschungsgruppen mit begrenzten Ressourcen. Insgesamt hat das System gezeigt, dass es in der Lage ist, Herausforderungen im Bereich
der Bioinformatik zu bewältigen und stellt somit ein wertvolles Werkzeug für Forscher in diesem Bereich dar. Die vorliegende Arbeit leistet mehrere wichtige Beiträge
zur Beantwortung von Forschungsfragen im Zusammenhang mit dem Entwurf, der
Implementierung und der Optimierung von Software-Systemen fĂĽr die Bioinformatik unter Verwendung von Prinzipien und Praktiken der Softwaretechnik. Unsere
Ergebnisse deuten darauf hin, dass die Einbindung dieser Technologien die Zuverlässigkeit, Skalierbarkeit, Leistungsfähigkeit, Effizienz und Produktivität bioinformatischer Software-Systeme erheblich verbessern kann
- …