Related papers: An approach to solve the coarse-grained Protein fo…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
Molecular docking is an important tool for structure-based drug design, accelerating the efficiency of drug development. Complex and dynamic binding processes between proteins and small molecules require searching and sampling over a wide…
Demonstrating the practical utility of Noisy Intermediate-Scale Quantum (NISQ) hardware for recurrent tasks in Computer-Aided Drug Discovery is of paramount importance. We tackle this challenge by performing three-dimensional protein…
We present a computational scheme for predicting the ligands that bind to a pocket of known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations and…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
We show that protein sequences can be thought of as sentences in natural language processing and can be parsed using the existing Quantum Natural Language framework into parameterized quantum circuits of reasonable qubits, which can be…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…
The development of tailored materials for specific applications is an active field of research in chemistry, material science and drug discovery. The number of possible molecules that can be obtained from a set of atomic species grow…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Charged particle reconstruction or track reconstruction is one of the most crucial components of pattern recognition in high-energy collider physics. It is known to entail enormous consumption of computing resources, especially when the…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
Drug discovery has become a main challenge in our society, following the Covid-19 pandemic. Even pharmaceutical companies are already using computing to accelerate drug discovery. They are increasingly interested in Quantum Computing with a…
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
With the advent of novel quantum computing technologies, and the knowledge that such technology might be used to fundamentally change computing applications, a prime opportunity has presented itself to investigate the practical application…
A new approach to efficient quantum computation with probabilistic gates is proposed and analyzed in both a local and non-local setting. It combines heralded gates previously studied for atom or atom-like qubits with logical encoding from…