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Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant…

The viability of a new drug molecule is a time and resource intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibitor…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…

Prediction of ligand binding sites of proteins is a fundamental and important task for understanding the function of proteins and screening potential drugs. Most existing methods require experimentally determined protein holo-structures as…

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep…

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereo-isomers, even at very low temperatures. In this paper we discuss the different approaches for the manipulation of the motion of…

Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…

All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

Pocket representations play a vital role in various biomedical applications, such as druggability estimation, ligand affinity prediction, and de novo drug design. While existing geometric features and pretrained representations have…

The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…

Multi-robot systems, particularly mobile manipulators, face challenges in control coordination and dynamic stability when working together. To address this issue, this study proposes MobiDock, a modular self-reconfigurable mobile…

Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…

A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…

Molecular dynamics (MD) is a central computational tool in physics, chemistry, and biology, enabling quantitative prediction of experimental observables as expectations over high-dimensional molecular distributions such as Boltzmann…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

We have developed an analytical, ligand-specific and scalable algorithm that detects a "signature" of the 3D binding site of a given ligand in a protein 3D structure. The said signature is a 3D motif in the form of an irregular tetrahedron…

We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models…