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While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative…
Electrospray ion-beam deposition (ES-IBD) is a versatile tool to study structure and reactivity of molecules from small metal clusters to large protein assemblies. It brings molecules gently into the gas phase where they can be accurately…
With recent rapid growth in online shopping, AI-powered Engagement Surfaces (ES) have become ubiquitous across retail services. These engagement surfaces perform an increasing range of functions, including recommending new products for…
Development of scoring functions (SFs) used to predict protein-ligand binding energies requires high-quality 3D structures and binding assay data for training and testing their parameters. In this work, we show that one of the widely-used…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Rebinding of dissociated ligands from cell surface proteins can confound quantitative measurements of dissociation rates important for characterizing the affinity of binding interactions. This can be true also for in vitro techniques such…
Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
Electrospray ion beam deposition (ESIBD) is the intact, chemically selective deposition of molecular ions on surfaces in vacuum. Here, we present a general method and dedicated instrumentation for ESIBD-based cryoEM sample preparation of…
Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…
Motivation: Protein-ligand affinity prediction is an important part of structure-based drug design. It includes molecular docking and affinity prediction. Although molecular dynamics can predict affinity with high accuracy at present, it is…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
We present results of testing of the ability of eleven popular scoring functions to predict native docked positions using a recently developed method [1] for estimation the entropy contributions of relative motions to protein-ligand binding…
In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
Most machine learning models for materials science rely on descriptors based on materials compositions and structures, even though the chemical bond has been proven to be a valuable concept for predicting materials properties. Over the…
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…