Gating and intermolecular interactions in ligand-protein association: coarse-grained modeling of HIV-1 protease

M Kang, C Roberts, Y Cheng… - Journal of chemical theory …, 2011 - ACS Publications
Most biological processes are initiated or mediated by the association of ligands and
proteins. This work studies multistep, ligand–protein association processes by Brownian …

Application of Graph Theory and Automata Modeling for the Study of the Evolution of Metabolic Pathways with Glycolysis and Krebs Cycle as Case Studies

C De Las Morenas Mateos, R Lahoz-Beltra - Computation, 2023 - mdpi.com
Today, graph theory represents one of the most important modeling techniques in biology.
One of the most important applications is in the study of metabolic networks. During …

Computer-guided surface engineering for enzyme improvement

M Wilding, C Scott, AC Warden - Scientific Reports, 2018 - nature.com
Protein engineering strategies are often guided by our understanding of how the structure of
a protein determines its function. However, our understanding is generally restricted to small …

A cellular automaton model of Schistosoma japonicum infection

C Wan, Y Liu, XM Tu, YY Zhang, JM Xu, DD Lin, JP Luo… - Acta tropica, 2013 - Elsevier
Due to the life cycle complexity of Schistosoma japonicum and the characteristics of
schistosomias is immuno-epidemiology, it is very challenging to give a group of certain rules …

Application of Graph Theory and Automata Modeling for the Study of the Evolution of Metabolic Pathways with Glycolysis and Krebs Cycle as Case Studies

CL Morenas Mateos, R Lahoz Beltra - 2023 - docta.ucm.es
Today, graph theory represents one of the most important modeling techniques in biology.
One of the most important applications is in the study of metabolic networks. During …

A core process in receptor function, general anesthesia, sleep, and aging

LB Kier, PW Slattum - Chemistry & Biodiversity, 2012 - Wiley Online Library
The diffusion of ligands and proteins was proposed to be guided by chreodes in water
organized by protein‐surface side chains with varying hydropathic states. These chreodes …

A core molecular theory of sleep and aging

L B. Kier - Current Computer-Aided Drug Design, 2012 - benthamdirect.com
Models of water in the presence of amino acid side chains have revealed significant
variability in the local water structure, reflecting the variations in the hydropathic states of the …

Evolution of 'Ligand‐Diffusion Chreodes' on Protein‐Surface Models: A Genetic‐Algorithm Study

SA Marashi, M Kargar, A Katanforoush… - Chemistry & …, 2007 - Wiley Online Library
Lattice models have been previously used to model ligand diffusion on protein surfaces.
Using such models, it has been shown that the presence of pathways (or 'chreodes') of …

A review of recent studies relating ligand diffusion, general anesthesia, and sleep.

LB Kier - AANA journal, 2008 - search.ebscohost.com
This review article presents 3 theories related to ligand diffusion, general anesthesia and
sleep. The first theory describes the diffusion of molecules across a protein surface to a …

Water Chreodes and the Mechanisms of Ligand Diffusion, General Anesthesia, and Sleep

LB Kier - Biochemistry Research International, 2011 - Wiley Online Library
The concept of the presence of passageways, chreodes, created by the influence of the
hydropathic states of amino acid side chains on the surface water of proteins, has been …