Related papers: MuCO: Generative Peptide Cyclization Empowered by …
Peptides are formed by the dehydration condensation of multiple amino acids. The primary structure of a peptide can be represented either as an amino acid sequence or as a molecular graph consisting of atoms and chemical bonds. Previous…
Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Molecule optimization is a critical step in drug development to improve desired properties of drug candidates through chemical modification. We developed a novel deep generative model Modof over molecular graphs for molecule optimization.…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
Conformal prediction offers finite-sample coverage guarantees under minimal assumptions. However, existing methods treat the entire modeling process as a black box, overlooking opportunities to exploit and understand modular structure. We…
Molecular docking is a crucial phase in drug discovery, involving the precise determination of the optimal spatial arrangement between two molecules when they bind. The such analysis, the 3D structure of molecules is a fundamental…
In the present paper, an integrated paradigm for topology optimization on complex surfaces with arbitrary genus is proposed. The approach is constructed based on the two-dimensional (2D) Moving Morphable Component (MMC) framework, where a…
Within the framework of computational plasticity, recent advances show that the quasi-static response of an elasto-plastic structure under cyclic loadings may exhibit a time multiscale behaviour. In particular, the system response can be…
We present a method to include robustness into a multi-criteria optimization (MCO) framework for intensity-modulated proton therapy (IMPT). The approach allows one to simultaneously explore the trade-off between different objectives as well…
Combinatorial Optimization (CO) addresses many important problems, including the challenging Maximum Independent Set (MIS) problem. Alongside exact and heuristic solvers, differentiable approaches have emerged, often using continuous…
Liposomes that achieve a heterogeneous and spatially organized surface through phase separation have been recognized to be a promising platform for delivery purposes. However, their design and optimization through experimentation can be…
Cyclic molecules are ubiquitous across applications in chemistry and biology. Their restricted conformational flexibility provides structural pre-organization that is key to their function in drug discovery and catalysis. However, reliably…
Multi-objective probabilistic model checking provides a way to verify several, possibly conflicting, quantitative properties of a stochastic system. It has useful applications in controller synthesis and compositional probabilistic…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Mixed-integer convex programming (MICP) has seen significant algorithmic and hardware improvements with several orders of magnitude solve time speedups compared to 25 years ago. Despite these advances, MICP has been rarely applied to…
Although various structural optimization techniques have a sound mathematical basis, the practical constructability of optimal designs poses a great challenge in the manufacturing stage. Currently, there is only a limited number of unified…
Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only…
An efficient computational approach for optimal reconstructing parameters of binary-type physical properties for models in biomedical applications is developed and validated. The methodology includes gradient-based multiscale optimization…