A5051687648- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- Molecular spectroscopy and chirality
- Spectroscopy and Quantum Chemical Studies
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Advanced Chemical Physics Studies
- Mass Spectrometry Techniques and Applications
- RNA and protein synthesis mechanisms
- Photoreceptor and optogenetics research
- DNA and Nucleic Acid Chemistry
- Glycosylation and Glycoproteins Research
- Machine Learning in Materials Science
- Analytical Chemistry and Chromatography
- Photochemistry and Electron Transfer Studies
- Photosynthetic Processes and Mechanisms
- Chemical Synthesis and Analysis
- Chemistry and Chemical Engineering
- Molecular Junctions and Nanostructures
- Various Chemistry Research Topics
- Synthesis and Properties of Aromatic Compounds
- Innovative Microfluidic and Catalytic Techniques Innovation
- Bioinformatics and Genomic Networks
- Phase Equilibria and Thermodynamics
- Protein Degradation and Inhibitors
University of Nottingham
2016-2025
Park University
2007-2025
University of Nottingham Ningbo China
2024
Smiths Detection (United States)
2020-2023
Royal Society of Chemistry
2023
Shanghai Jiao Tong University
2020-2023
Sheffield Hallam University
2019
Synchrotron soleil
2019
University of California, Irvine
2010
University of Warwick
1997-2009
Post translational modifications (PTMs) occur in the vast majority of proteins and are essential for function. Prediction sequence location PTMs enhances functional characterisation proteins. Glycosylation is one type PTM, implicated protein folding, transport We use random forest algorithm pairwise patterns to predict glycosylation sites. identify surrounding sites an odds ratio weight their propensity association with modified residues. Our prediction program, GPP (glycosylation program),...
In this paper different floating oscillator models for describing the amide I band of peptides and proteins are compared with density functional theory (DFT) calculations. Models variation frequency shifts oscillators nearest-neighbor coupling between them respect to conformation constructed from DFT normal mode calculations on N-acetyl-glycine-N′-methylamide. The calculated frequencies those obtained existing electrostatic models. Furthermore, a new transition charge model is presented. We...
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations in a fluctuating environment. Herein we present novel machine learning protocol that uses few key structural descriptors to rapidly predict amide I various proteins and agrees well with experiment. Its transferability enabled us distinguish...
A good docking algorithm requires an energy function that is selective, in it clearly differentiates correctly docked structures from misdocked ones, and efficient, meaning a structure can be identified quickly. We assess the selectivity efficiency of broad spectrum functions, derived systematic modifications CHARMM param19/toph19 function. In particular, we examine effects dielectric constant, solvation model, scaling surface charges, reduction van der Waals repulsion, nonbonded cutoffs....
Proteins have characteristic circular dichroism spectra in the far-ultraviolet, depending on their secondary structure content. Perhaps most distinctive spectrum is that of α-helical proteins, with an intense positive band centered about 190 nm and a negative, double-peaked minima at 208 220 nm. Traditionally, calculations such from first principles involved parametrizations charge distributions associated electronic states transitions constituent chromophoric groups. The amide group...
We present a comparative assessment of several state-of-the-art machine learning tools for mining drug data, including support vector machines (SVMs) and the ensemble decision tree methods boosting, bagging, random forest, using eight data sets two descriptors. demonstrate, by rigorous multiple comparison statistical tests, that these techniques can provide consistent improvements in predictive performance over single trees. However, within methods, there is no clearly best-performing...
Abstract Motivation: Circular dichroism (CD) is widely used in studies of protein folding. The CD spectrum a can be estimated from its structure alone, using the well-established matrix method. In last decade, related spectroscopy, linear (LD), has been increasingly applied to study orientation proteins solution. However, method calculations LD spectra have not presented before. DichroCalc makes both and available an easy-to-use fashion. Results: without registration calculates variety...
Single-atom catalysts (SACs) have emerged as attractive materials for the electrocatalytic carbon dioxide reduction (ECO2R). Dual-atom (DACs), an extension of SACs, exhibit more compelling functionalities due to synergistic effects between adjacent metal atoms. However, rational design, clear coordination mode, and in-depth understanding heteronuclear dual-atom mechanisms remain elusive. Herein, a Ni-Ag catalyst loaded on defective nitrogen-rich porous carbon, denoted Ni-Ag/PC-N, was...
We assess the efficiency of molecular dynamics (MD), Monte Carlo (MC), and genetic algorithms (GA) for docking five representative ligand–receptor complexes. All three employ a modified CHARMM-based energy function. The are also compared with an established algorithm, AutoDock. receptors kept rigid while flexibility ligands is permitted. To test algorithms, two search spaces used: 11-Å-radius sphere 2.5-Å-radius sphere, both centered on active site. find MD most efficient in case large...
Abstract We present DESTRUCT, a new method of protein secondary structure prediction, which achieves three‐state accuracy (Q 3 ) 79.4% in cross‐validated trial on nonredundant set 513 proteins. An iterative cascade–correlation neural networks is used to predict both and ψ dihedral angles, with predicted values enhancing the subsequent iteration. Predictive accuracies 80.7% 81.7% are achieved CASP4 CASP5 targets, respectively. Our approach significantly more accurate than other contemporary...
The molecular interactions between the CeIV -substituted Keggin anion [PW11 O39 Ce(OH2 )4 ]3- (CeK) and hen egg-white lysozyme (HEWL) were investigated by dynamics simulations. analysis of CeK was compared with dimer [(PW11 )2 Ce]10- (CeK2 ) ZrIV Lindqvist [W5 O18 Zr(OH2 )(OH)]3- (ZrL) to understand how POM features such as shape, size, charge, or type incorporated metal ion influence POM⋅⋅⋅protein interactions. Simulations revealed two regions protein in which interacts strongly: cationic...
Of the many roles that solvent plays, its influence on molecular electronic structure is perhaps one of more challenging phenomena to study. In this study, effect solvation spectrum formamide investigated. Ab initio complete-active-space self-consistent field (CASSCF) and multiconfigurational second-order perturbation theory (CASPT2) methods are used compute ground- excited-state energies complexed with one, two, three water molecules. addition, a semicontinuum approach employed, in which...
Here we investigate the structures and energetics of interactions between aromatic (Phe or Tyr) basic (Lys Arg) amino acids in α-helices. Side chain interaction energies are measured using helical peptides, by quantifying their helicities with circular dichroism at 222 nm interpreting results Lifson−Roig-based helix/coil theory. A difficulty working Tyr is that ring perturbs CD spectrum, giving an incorrect helicity. We calculated effect on deriving intensities bands directly from electronic...