arXiv subjects

Duc Duy Nguyen

Publications and source records attributed to Duc Duy Nguyen.

22 records · Page 2Linked to original sources

arXiv2017

Rigidity strengthening is a vital mechanism for protein-ligand binding

Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug design and protein design. Based on large scale data sets, we show that protein rigidity strengthening or flexibility reduction is a pivoting mechanism in protein-ligand binding. Our approach based solely on rigidity is able to unveil a surprisingly long range contribution of four residue layers to protein-ligand binding, which has a ramification for drug and protein design. Additionally, the present work reveals that among various pairwise interactions, the short range ones within the distance of the van der Waals diameter are most important. It is found that the present approach outperforms all the other state-of-the-art scoring functions for protein-ligand binding affinity predictions of two benchmark data sets

q-bio.BM↗

arXiv2016

Generalized flexibility-rigidity index

Flexibility-rigidity index (FRI) has been developed as a robust, accurate and efficient method for macromolecular thermal fluctuation analysis and B-factor prediction. The performance of FRI depends on its formulations of rigidity index and flexibility index. In this work, we introduce alternative rigidity and flexibility formulations. The structure of the classic Gaussian surface is utilized to construct a new type of rigidity index, which leads to a new class of rigidity densities with the classic Gaussian surface as a special case. Additionally, we introduce a new type of flexibility index based on the domain indicator property of normalized rigidity density. These generalized FRI (gFRI) methods have been extensively validated by the B-factor predictions of 364 proteins. Significantly outperforming the classic Gaussian network model (GNM), gFRI is a new generation of methodologies for accurate, robust and efficient analysis of protein flexibility and fluctuation. Finally, gFRI based molecular surface generation and flexibility visualization are demonstrated.

q-bio.BM↗

arXiv2016

The impact of surface area, volume, curvature and Lennard-Jones potential to solvation modeling

This paper explores the impact of surface area, volume, curvature and Lennard-Jones potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each others, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the Lennard-Jones (LJ) potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature and LJ potential are less than 0.42 kcal/mol for all test sets.

q-bio.QM↗

arXiv2011

First cohomology for finite groups of Lie type: simple modules with small dominant weights

Let $k$ be an algebraically closed field of characteristic $p > 0$, and let $G$ be a simple, simply connected algebraic group defined over $\mathbb{F}_p$. Given $r \geq 1$, set $q=p^r$, and let $G(\mathbb{F}_q)$ be the corresponding finite Chevalley group. In this paper we investigate the structure of the first cohomology group $H^1(G(\mathbb{F}_q),L(λ))$ where $L(λ)$ is the simple $G$-module of highest weight $λ$. Under certain very mild conditions on $p$ and $q$, we are able to completely describe the first cohomology group when $λ$ is less than or equal to a fundamental dominant weight. In particular, in the cases we consider, we show that the first cohomology group has dimension at most one. Our calculations significantly extend, and provide new proofs for, earlier results of Cline, Parshall, Scott, and Jones, who considered the special case when $λ$ is a minimal nonzero dominant weight.

math.GR↗