Related papers: iMOLSDOCK : induced-fit docking using mutually ort…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e.,…
In recent years, machine learning (ML) methods have emerged as promising alternatives for molecular docking, offering the potential for high accuracy without incurring prohibitive computational costs. However, recent studies have indicated…
As powerful pre-trained vision-language models (VLMs) like CLIP gain prominence, numerous studies have attempted to combine VLMs for downstream tasks. Among these, prompt learning has been validated as an effective method for adapting to…
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…
Understanding the structure of the protein-ligand complex is crucial to drug development. Existing virtual structure measurement and screening methods are dominated by docking and its derived methods combined with deep learning. However,…
We report on a new capability added to our general relativistic radiation-magnetohydrodynamics code, Cosmos++: an implicit Monte Carlo (IMC) treatment for radiation transport. The method is based on a Fleck-type implicit discretization of…
Energy evaluation using fast Fourier transforms enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods efficient acceleration is achieved only in either…
We propose a benchmark to study surrogate model accuracy for protein-ligand docking. We share a dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million "in-stock" molecules over…
Materials that respond to external stimuli by expanding or contracting provide a transduction route that integrates sensing and actuation powered directly by the stimuli. This motivates us to build colloidal scale robots using these…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
Molecular docking is a crucial step in the development of new drugs as it guides the positioning of a small molecule (ligand) within the pocket of a target protein. In the literature, a feasibility study explored the potential of D-Wave…
Quadrupedal locomotion is a complex, open-ended problem vital to expanding autonomous vehicle reach. Traditional reinforcement learning approaches often fall short due to training instability and sample inefficiency. We propose a novel…
Data transmission rate in molecular communication systems can be improved by using multiple transmitters and receivers. In molecular multiple-input multiple-output (MIMO) systems which use only single type of molecules, the performance at…
Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
In this paper we provide results on using integer programming (IP) and constraint programming (CP) to search for sets of mutually orthogonal latin squares (MOLS). Both programming paradigms have previously successfully been used to search…
Due to the need for higher reliability and performance from RF circuits, multi-port reflectometers are increasingly used as low-overhead impedance monitors. In this work, using periodic structures as multi-ports is proposed. Periodic…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…
Position sensitive detectors (PSDs) offer possibility to track single active marker's two (or three) degrees of freedom (DoF) position with a high accuracy, while having a fast response time with high update frequency and low latency, all…
Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity…