Related papers: An approach to solve the coarse-grained Protein fo…
Quantum-chemical fragmentation methods offer an efficient approach for the treatment of large proteins, in particular if local target quantities such as protein--ligand interaction energies, enzymatic reaction energies, or spectroscopic…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
Quantum annealing offers a promising paradigm for solving NP-hard combinatorial optimization problems, but its practical application is severely hindered by two challenges: the complex, manual process of translating problem descriptions…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial…
Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current…
Quantum computing and modern tensor-based computing have a strong connection, which is especially demonstrated by simulating quantum computations with tensor networks. The other direction is less studied: quantum computing is not often…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
Molecular docking is a critical computational method in drug discovery used to predict the binding conformation and orientation of a ligand within a protein's binding site. Mapping this challenge onto a graph-based problem, specifically the…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
In the traditional random-conformational-search model, various hypotheses with a series of meta-stable intermediate states were often proposed to resolve the Levinthal paradox. Here we introduce a quantum strategy to formulate protein…
Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently,…
Proteins play a central role in biology from immune recognition to brain activity. While major advances in machine learning have improved our ability to predict protein structure from sequence, determining protein function from structure…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
Many artificial intelligence (AI) problems naturally map to NP-hard optimization problems. This has the interesting consequence that enabling human-level capability in machines often requires systems that can handle formally intractable…
Modern quantum annealers can find high-quality solutions to combinatorial optimisation objectives given as quadratic unconstrained binary optimisation (QUBO) problems. Unfortunately, obtaining suitable QUBO forms in computer vision remains…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
Fitting geometric models onto outlier contaminated data is provably intractable. Many computer vision systems rely on random sampling heuristics to solve robust fitting, which do not provide optimality guarantees and error bounds. It is…
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…