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Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Data science has emerged from the proliferation of digital data, coupled with advances in algorithms, software and hardware (e.g., GPU computing). Innovations in structural biology have been driven by similar factors, spurring us to ask:…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Open Science is a paradigm in which scientific data, procedures, tools and results are shared transparently and reused by society as a whole. The initiative known as the European Open Science Cloud (EOSC) is an effort in Europe to provide…
Scientific research increasingly depends on robust and scalable IT infrastructures to support complex computational workflows. With the proliferation of services provided by research infrastructures, NRENs, and commercial cloud providers,…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
Data mining is a recognized predictive tool in a variety of areas ranging from bioinformatics and drug design to crystal structure prediction. In the present study, an electronic structure implementation has been combined with structural…
Causal structure learning refers to a process of identifying causal structures from observational data, and it can have multiple applications in biomedicine and health care. This paper provides a practical review and tutorial on scalable…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…