Search Results: atomic

Graph Theoretical Representation of Atomic Asymmetry and Molecular Chirality of Benzenoids in Two-Dimensional Space

dx.plos.org/10.1371/journal.pone.0102043
In order to explore atomic asymmetry and molecular chirality in 2D space, benzenoids composed of 3 to 11 hexagons in 2D space were enumerated in our laboratory. These benzenoids are regarded as planar connected polyhexes and have no internal holes; that is, their internal regions are filled with hexagons. The produced dataset was composed of 357,968 benzenoids, including more than 14 million atoms. Rather than simply labeling the huge number of atoms as being either symmetric or asymm...

HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

dx.plos.org/10.1371/journal.pone.0006701
Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimiz...

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

dx.plos.org/10.1371/journal.pcbi.1004999
Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichio...

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

dx.plos.org/10.1371/journal.pone.0114042
A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of at...

The Ol' Switcheroo Shows How an RNA Enzyme Splices Itself

dx.plos.org/10.1371/journal.pbio.0030310

Density functional theory study the effects of oxygen-containing functional groups on oxygen molecules and oxygen atoms adsorbed on carbonaceous materials

dx.plos.org/10.1371/journal.pone.0173864
Density functional theory was used to study the effects of different types of oxygen-containing functional groups on the adsorption of oxygen molecules and single active oxygen atoms on carbonaceous materials. During gasification or combustion reactions of carbonaceous materials, oxygen-containing functional groups such as hydroxyl(-OH), carbonyl(-CO), quinone(-O), and carboxyl(-COOH) are often present on the edge of graphite and can affect graphite’s chemical properties. When oxyge...

G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation

dx.plos.org/10.1371/journal.pone.0155816
The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic m...

Cavities and Atomic Packing in Protein Structures and Interfaces

dx.plos.org/10.1371/journal.pcbi.1000188
A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependenc...

Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces

dx.plos.org/10.1371/journal.pone.0059737
Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kin...

A Method for Finding Metabolic Pathways Using Atomic Group Tracking

dx.plos.org/10.1371/journal.pone.0168725
A fundamental computational problem in metabolic engineering is to find pathways between compounds. Pathfinding methods using atom tracking have been widely used to find biochemically relevant pathways. However, these methods require the user to define the atoms to be tracked. This may lead to failing to predict the pathways that do not conserve the user-defined atoms. In this work, we propose a pathfinding method called AGPathFinder to find biochemically relevant metabolic pathways b...

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