Related papers: In Silico Tools in PROTACs design
Since the turn of the millennium, computational modelling of biological systems has evolved remarkably and sees matured use spanning basic and clinical research. While the topic of the peri-millennial debate about the virtues and…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools…
The physics of glasses can be studied from many viewpoints, from material scientists interested in the development of new materials to statistical physicists inventing new theoretical tools to deal with disordered systems. In these lectures…
Artificial intelligence (AI) has sparked immense interest in drug discovery, but most current approaches only digitize existing high-throughput experiments. They remain constrained by conventional pipelines. As a result, they do not address…
In this paper, we focus on the design and verification of timed automata (TA). We introduce a new method for assisting construction and verification of TA models along with a tool implementing the proposed method, i.e., ATAC: Automated…
Despite improved rational drug design and a remarkable progress in genomic, proteomic and high-throughput screening methods, the number of novel, single-target drugs fell much behind expectations during the past decade. Multi-target drugs…
The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
Domain-aware machine learning (ML) models have been increasingly adopted for accelerating small molecule therapeutic design in the recent years. These models have been enabled by significant advancement in state-of-the-art artificial…
Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early…
Prototyping is one of the core activities of User-Centered Design (UCD) processes and an integral component of Human-Computer Interaction (HCI) research. For many years, prototyping was synonym of paper-based mockups and only more recently…
In Silico Clinical Trials (ISTC), i.e., clinical experimental campaigns carried out by means of computer simulations, hold the promise to decrease time and cost for the safety and efficacy assessment of pharmacological treatments, reduce…
The design of complex materials and the formation of specific patterns often arise from the properties of the individual building blocks. In this respect, colloidal systems offer a unique opportunity because nowadays they can be synthesized…
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…
The miniaturization and integration of electronic circuitry has not only made the enormous increase in performance of semiconductor devices possible but also spawned a myriad of new products and applications ranging from a cellular phone to…
In this paper, we use Time Scale Calculus (TSC) to formulate and solve pharmacokinetic models exploring multiple dose dynamics. TSC is a mathematical framework that allows the modeling of dynamical systems comprising continuous and discrete…
Nanomaterials possess a wide range of potential applications due to their novel properties compared to bulk matter, but these same properties may represent an unknown risk to health. Experimental safety testing cannot keep pace with the…
Dream of developing molecule-based logic and memory device is more than 70-year-old. Presently, molecule-based devices are also considered for quantum computation hardware. The recent studies have shown the molecule connected to metal leads…
Proteolysis-targeting chimeras (PROTACs) represent a promising therapeutic modality that induces targeted protein degradation by hijacking the ubiquitin-proteasome system. However, rational PROTAC design remains challenging due to the…
Optimal experimental design approaches are seldom used in pre-clinical drug discovery. Main reasons for this lack of use are that available software tools require relatively high insight in optimal design theory, and that the…