Related papers: In Silico Tools in PROTACs design
The efficacy of a drug depends on its binding affinity to the therapeutic target and pharmacokinetics. Deep learning (DL) has demonstrated remarkable progress in predicting drug efficacy. We develop MolDesigner, a human-in-the-loop web…
De novo molecule generation often results in chemically unfeasible molecules. A natural idea to mitigate this problem is to bias the search process towards more easily synthesizable molecules using a proxy for synthetic accessibility.…
Traditional robotic manipulator design methods require extensive, time-consuming, and manual trial and error to produce a viable design. During this process, engineers often spend their time redesigning or reshaping components as they…
Designing compounds with desired properties is a key element of the drug discovery process. However, measuring progress in the field has been challenging due to the lack of realistic retrospective benchmarks, and the large cost of…
The popularity of accessibility research has grown recently, improving digital inclusion for people with disabilities. However, researchers, including those who have disabilities, have attempted to include people with disabilities in all…
Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex…
Building of tools--from simple prototypes to industrial-strength applications--is a pervasive activity in academic research. When proposing a new technique for software maintenance, effective tool support is typically required to…
Proteolysis-Targeting Chimeras (PROTACs) represent a novel class of small molecules which are designed to act as a bridge between an E3 ligase and a disease-relevant protein, thereby promoting its subsequent degradation. PROTACs are…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Drug promiscuity and polypharmacology are much discussed topics in pharmaceutical research. Drug repositioning applies established drugs to new disease indications with increasing success. As polypharmacology, defined a drug's ability to…
System-level design, once the province of board designers, has now become a central concern for chip designers. Because chip design is a less forgiving design medium -- design cycles are longer and mistakes are harder to correct --…
The introduction of new tools in people's workflow has always been promotive of new creative paths. This paper discusses the impact of using computational tools in the performance of creative tasks, especially focusing on graphic design.…
During the last decades, medical observations and multiscale data concerning tumor growth are mounting. At the same time, contemporary imaging techniques well established in clinical practice, provide a variety of information on real-time,…
Over the past decade a large family of spintronic devices have been proposed as candidates for replacing CMOS for future digital logic circuits. Using the recently developed Modular Approach framework, we investigate and identify the…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to…
This paper introduces SiQAD, a computer-aided design tool enabling the rapid design and simulation of atomic silicon dangling bond quantum dot patterns capable of computational logic. Several simulation tools are included, each able to…
ParSplice D. Perez, E. D. Cubuk, A. Waterland, E. Kaxiras, and A. F. Voter, Long-Time Dynamics through Parallel Trajectory Splicing, Journal of Chemical Theory and Computation, 2016 is a molecular dynamics method for parallel-in-time…
Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the…