Related papers: A Novel P-bit-based Probabilistic Computing Approa…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Protein folding processes are a vital aspect of molecular biology that is hard to simulate with conventional computers. Quantum algorithms have been proven superior for certain problems and may help tackle this complex life science…
This paper presents a novel Differential Evolution algorithm for protein folding optimization that is applied to a three-dimensional AB off-lattice model. The proposed algorithm includes two new mechanisms. A local search is used to improve…
Domain-specific hardware to solve computationally hard optimization problems has generated tremendous excitement. Here, we evaluate probabilistic bit (p-bit) based Ising Machines (IM) on the 3-regular 3-Exclusive OR Satisfiability (3R3X),…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…
Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the energy landscape of natural proteins. Finding low-energy…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
The fold recognition methods are promissing tools for capturing the structure of a protein by its amino acid residues sequence but their use is still restricted by the needs of huge computational resources and suitable efficient algorithms…
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…
Photonic Ising Machines constitute an emergent new paradigm of computation, geared towards tackling combinatorial optimization problems that can be reduced to the problem of finding the ground state of an Ising model. Spatial Photonic Ising…
Protein folding is a central challenge in computational biology, with important applications in molecular biology, drug discovery and catalyst design. As a hard combinatorial optimisation problem, it has been studied as a potential target…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
The D-Wave quantum annealers make it possible to obtain high quality solutions of NP-hard problems by mapping a problem in a QUBO (quadratic unconstrained binary optimization) or Ising form to the physical qubit connectivity structure on…
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…
Probabilistic Bit (P-Bit) device serves as the core hardware for implementing Ising computation. However, the severe intrinsic variations of stochastic P-Bit devices hinder the large-scale expansion of the P-Bit array, significantly…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
The peptide-protein docking problem is an important problem in structural biology that facilitates rational and efficient drug design. In this work, we explore modeling and solving this problem with the quantum-amenable quadratic…
We propose a hybrid classical-quantum digitized-counterdiabatic algorithm to tackle the protein folding problem on a tetrahedral lattice. Digitized-counterdiabatic quantum computing is a paradigm developed to compress quantum algorithms via…
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,…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…