Related papers: Predicting 3D RNA Folding Patterns via Quadratic B…
Molecular docking, which aims to find the most stable interacting configuration of a set of molecules, is of critical importance to drug discovery. Although a considerable number of classical algorithms have been developed to carry out…
In the era of quantum computing, the emergence of quantum computers and subsequent advancements have led to the development of various quantum algorithms capable of solving linear equations and eigenvalues, surpassing the pace of classical…
Quantum computing has emerged as a promising alternative for solving combinatorial optimization problems. The standard approach for encoding optimization problems on quantum processing units (QPUs) involves transforming them into their…
Quantum computing offers significant potential for solving NP-hard combinatorial (optimization) problems that are beyond the reach of classical computers. One way to tap into this potential is by reformulating combinatorial problems as a…
We propose an algorithm inspired by optical coherent Ising machines to solve the problem of polynomial unconstrained binary optimization (PUBO). We benchmark the proposed algorithm against existing PUBO algorithms on the extended…
Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…
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…
We present a novel formulation of structural design optimization problems specifically tailored to be solved by quantum annealing (QA). Structural design optimization aims to find the best, i.e., material-efficient yet high-performance,…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
With the applications of quantum computing becoming more and more widespread, finding ways that allow end users without experience in the field to apply quantum computers to solve their individual problems is becoming a crucial task.…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
Leveraging quantum computers for optimization problems holds promise across various application domains. Nevertheless, utilizing respective quantum computing solvers requires describing the optimization problem according to the Quadratic…
As contemporary quantum computers do not possess error correction, any calculation performed by these devices can be considered an involuntary approximation. To solve a problem on a quantum annealer, it has to be expressed as an instance of…