Model conformational. Medical search. Frequent questions

The recent improvements of such parameters have made them suitable for the analysis of nucleic acids and for characterizing conformational changes in RNA molecules. (loria.fr)

We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. (nist.gov)
These simulations generate conformational ensembles (trajectories) to capture the motion of systems. (loria.fr)
In this PhD the goal is to design and implement a method for characterizing the conformational dynamics of protein-RNA complexes using the set of trajectories generated from MD simulations in a systematic way. (loria.fr)
proposed a probabilistic model that can simulate many features of biochemical experiments in terms of the reaction rate [7], although there are several differences between the biochemical experiments and the computational simulations on the model. (elsevierpure.com)
In particular, accelerated molecular dynamics simulations are suitable for conformational sampling when the unbound and bound states are separated by high energy barriers, provided that the acceleration parameters are carefully set to extensively sample the relevant conformations. (researcher-app.com)
We are studying the conformational changes of the extracellular domain using a combination of submicrosecond Molecular Dynamics simulations and Elastic Network Models. (ub.es)
Our research ideology is to work on theoretical models of complex fluids and use extensive computer simulations to inform and verify these models. (reading.ac.uk)
Our studies are performed using hybrid molecular dynamics/Monte Carlo simulations and theoretical modelling. (reading.ac.uk)
Here, we investigate the effect of an orthosteric and an allosteric antagonist on CCR2 dynamics by coupling long-timescale molecular dynamics simulations with Markov-state model theory. (iasp-pain.org)
AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. (openscience.org)
Monte Carlo simulations have been used to study three different models for linear, titrating polyelectrolytes in a salt-free environment: (i) a rigid polymer with rigid bonds (rigid rod), (ii) a flexible polymer with rigid bonds and (iii) a flexible polymer with flexible bonds. (lu.se)

We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. (nature.com)
Our model, based on time-independent component analysis (tICA) and protein graph connectivity network, was able to identify multiple residues, exhibiting long-distance coupling with the RBD opening dynamics. (biorxiv.org)
We applied time-independent component analysis (tICA) and protein connectivity network model, on all-atom molecular dynamics trajectories, to identify key non-RBD residues, playing crucial role in the conformational transition facilitating spike-receptor binding and infection of human cell. (biorxiv.org)
The main goal of this PhD project is to elucidate the conformational dynamics of protein-RNA complexes and to develop a method for understanding their allosteric communications. (loria.fr)
The candidate will be supervised by Yasaman Karami (Inria researcher) with expertise in analyzing proteins conformational dynamics and drug design [1,2], and Malika SmailTabonne (associate professor, University of Lorraine) expert in machine learning. (loria.fr)
Therefore, characterizing the structure, dynamics and conformational changes of biomolecules can help understand the molecular mechanisms of underlying diseases, and hopefully prevent them by designing drugs. (loria.fr)
While major improvements have been introduced with the breakthrough of artificial intelligence (AlphaFold2 [3]), predicting conformational dynamics of biomolecules is still challenging. (loria.fr)
On the other hand, computational approaches have been developed to investigate the conformational dynamics in proteins [4,5,6]. (loria.fr)
We performed targeted molecular dynamics simulation to obtain trajectory of conformational change from inactive to active form. (intechopen.com)
Protein dynamics play a critical role in ligand binding, and different models have been proposed to explain the relationships between protein motion and molecular recognition. (researcher-app.com)
In this internship the goal is to design and implement a generic analysis workflow to investigate the set of generated trajectories and dissect the conformational dynamics of different variants in a systematic way. (sfbi.fr)
The student will be supervised by Dr. Yasaman Karami, chargée de recherche Inria, with expertise in understanding proteins conformational dynamics and drug design [4,5]. (sfbi.fr)
A higher magnitude of conformational dynamics and variations are expected, especially for multi-domain proteins consisting of multiple structural domains. (biophysics.org)
The trajectory of the inter-gadolinium distance as predicted by molecular dynamics (MD) simulation is shown at the bottom, depicting drastic conformational changes of MurD. (biophysics.org)
We also investigated the conformational dynamics of the same protein by X-ray scattering, neutron scattering, and MD simulation. (biophysics.org)
A single chain stochastic model (Likhtman, 2005) represents a crucial step in hierarchical modelling, bridging the gap between multi-chain molecular dynamics simulation and the tube theory. (reading.ac.uk)
ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase. (lu.se)

Most docking programs in use account for a flexible ligand, and several attempt to model a flexible protein receptor. (wikipedia.org)
Genetic algorithms allow the exploration of a large conformational space - which is basically spanned by the protein and ligand jointly in this case - by representing each spatial arrangement of the pair as a "gene" with a particular energy. (wikipedia.org)
Although genetic algorithms are quite successful in sampling the large conformational space, many docking programs require the protein to remain fixed, while allowing only the ligand to flex and adjust to the active site of the protein. (wikipedia.org)
Most previous structural studies on S protein have been conducted at pH 8.0, but knowledge of the conformational propensities under both physiological and endosomal pH conditions is important to inform vaccine development. (nih.gov)
The proposed deep learning model will be set up to address the characterization of dynamic properties of protein-RNA interactions at the 3D level. (loria.fr)
Here, we present a study of ligand-binding processes associated with large conformational changes of a protein to elucidate the critical choices in ensemble-docking approaches for effective prediction of the binding geometry. (researcher-app.com)
Two study cases were selected in which binding involves different protein motions and intermolecular interactions and, accordingly, conformational selection and induced-fit mechanisms play different roles: binding of multiple ligands to the acetylcholine binding protein and highly specific binding of D-allose to the allose binding protein. (researcher-app.com)
Despite their importance in protein functions, the conformational states of proteins and their changes are often poorly understood, mainly because of the lack of an efficient strategy. (biophysics.org)
In our study, we exploited a paramagnetic lanthanide ion, Gd 3+ , in electron paramagnetic resonance (EPR) experiments and measured the inter-gadolinium distance distribution that reflects the conformational states of the protein. (biophysics.org)
The cover image for the 120/15 issue of Biophysical Journal conceptually shows the investigation of the conformational variation of a multidomain protein, MurD, based on the inter-gadolinium distance measurements. (biophysics.org)
Our study demonstrated that gadolinium tagging of specific positions on the protein enables EPR distance measurements for probing the conformational ensemble of the protein. (biophysics.org)
The data show that the protein enzyme MurD exists in a wide variety of the conformational states that were eliminated by ligand binding. (biophysics.org)
Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)
Because a uniform dielectric ionizable group in a protein relative to the pKa value of the continuum model is a very crude description of the highly same group in a small reference molecule in dilute aqueous heterogeneous protein interior, the dielectric coefficient, eP, solution. (lu.se)
The intrusion of lead into the lens may alter lens redox status and cause protein conformational changes that decrease lens transparency. (cdc.gov)

In this approach, proteins are typically held rigid, and the ligand is allowed to freely explore their conformational space. (wikipedia.org)
We find evidence for the selective allosteric activation and inhibition of Hsp90's conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90's complex allosteric mechanism of action. (nature.com)
Structural basis for ligand modulation of the CCR2 conformational landscape. (iasp-pain.org)

To overcome this problem we develop a method that combines a computational structural modeling (which delivers atomic-resolution structures) with experimental data (which provides information about the population of different states). (lu.se)

Because multi-domain proteins often undergo drastic conformational changes during their functional processes, information about their dynamic properties is essential to understand the mechanisms. (biophysics.org)

The aim of this work is to investigate, through a mathematical model, how the structural stability of different aggregated forms can influence the kinetics of prion replication. (sissa.it)
The method applies Bayesian probabilistic model to analyze scattering data from mixtures of oligomeric species, allows for a modeling large structural ensembles, can be used to assess uncertainty of all parameters and minimizes over-fitting. (lu.se)

To investigate the conformational change of c-Src tyrosine kinase, we applied network analysis to time series of correlation among residues. (intechopen.com)
The time series of correlation between residues during the conformational change generated by targeted molecular dynamic simulation. (intechopen.com)
With centrality measures such as betweenness centrality, degree centrality, and closeness centrality, we observed a few important residues that significantly contribute to the conformational change of c-Src tyrosine kinase for the different time steps. (intechopen.com)
b ) A schematic of the LTGF β -1 gene and the residues included in crystallization and model building. (iucr.org)
On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues. (lu.se)

The conformational analysis was performed utilizing FT-IR matrix isolation technique and theoretical methods such as density functional theory and ab initio calculations. (researchgate.net)
The theoretical models we are working with range from stochastic differential equations to partial differential equations to constitutive equations (tensor ODEs). (reading.ac.uk)

Recently we have shown that a coarse-grained model based on the primitive model, that has been used for modelling polyelectrolytes for over 30 years, works well for a range of IDPs where electrostatics governs the intra- and intermolecular interactions [1]. (lu.se)

Thus, the conformational preferences of a naphthyl xyloside, which initiates in vivo synthesis of antiproliferative glycosaminoglycans, have been studied by using NMR spectroscopy in a variety of solvents. (lu.se)
Three model dipeptides containing a dehydroalanine residue (Ala) at the C-terminal, Boc-X-Ala-NHCH3 [X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by 1H-NMR, IR, and CD spectroscopy. (iisc.ac.in)
A nuclear magnetic resonance spectroscopy and molecular modeling study. (unthsc.edu)
Carbon 1s photoelectron spectroscopy of the chlorinated methanes: Lifetimes and accurate vibrational lineshape models. (uib.no)
The structure of mixed methanol/chloroform clusters from core-level photoelectron spectroscopy and modeling. (uib.no)

Esposito, G. PDB2ENTROPY and PDB2TRENT: Conformational and Translational-Rotational Entropy from Molecular Ensembles. (lu.se)
The similar problem is faced when resolving conformational ensembles from small angle scattering data. (lu.se)

B ) Hsp90's nucleotide driven conformational cycle (Adopted from Penkler et al . (nature.com)
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU. (expasy.org)

These systems undergo conformational changes in response to different environmental conditions, such as mutations, changes in temperature or electrostatic potential, and binding to other molecules. (loria.fr)

Much of the work is then directed to investigating entanglement properties in different systems and thus informing simpler and coarser models. (reading.ac.uk)

The simulation results have much more similarities to the biochemical experiments results than ones on the previous model, which implies that the analysis of the model may give some insight about the reaction rate. (elsevierpure.com)

We are interested in microscopic modelling of the processes taking place at moving contact lines to understand the origin of the dynamic wetting effects in situations involving simple and complex interfaces, e.g. interfaces laden with polymers, particles and surfactants. (reading.ac.uk)

Recent improvements in using grid-based evaluation of energies, limiting the exploration of the conformational changes at only local areas (active sites) of interest, and improved tabling methods have significantly enhanced the performance of genetic algorithms and made them suitable for virtual screening applications. (wikipedia.org)

The model-based results suggest that prion strains with different conformational stability undergoing in vivo replication are characterizable in primis by means of different rates of breakage. (sissa.it)

The process is initiated by a down to up conformational change in the spike presenting the RBD to the receptor. (biorxiv.org)
In the nearest neighbor model the free energy change for each motif depends on the sequence of the motif and of its closest base-pairs. (wikipedia.org)
Conformational change of the AcrR regulator reveals a possible mechanism of induction. (expasy.org)
Conformational Change? (lu.se)

The kinetic variability introduced in the model by these two parameters allows us to reproduce the different characteristic features of the various strains (e.g., fibrils\\\' mean length) and is coherent with all experimental observations concerning strain-specific behavior. (sissa.it)

CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. (elifesciences.org)
Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. (elifesciences.org)

Complexes of Vps34, the sole class III PI3K member, produce PI 3-phosphate (PI(3)P) in the endolysosomal system and during autophagy to regulate vesicle-mediated sorting en route to lysosomes 1 . (nature.com)

During the conformational analysis the envelope (E) and twisted (T) ring shapes with the position of the fluorine atom and chloromethyl group in terms of axial/equatorial and cis/trans/gauche-/gauche+ positions were investigated utilizing MP2/aug-cc-pVTZ and DFT/B3LYP/aug-cc-pVTZ level of theory. (researchgate.net)
Synthesis and conformational analysis of a bridged anabasine and related compounds. (unthsc.edu)
Dive into the research topics of 'Synthesis and conformational analysis of a bridged anabasine and related compounds. (unthsc.edu)

We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)

On the basis of the [email protected]2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function. (researchgate.net)

This study presents convincing evidence, utilizing various biophysical techniques, to support a model for BTK activation that will be valuable for the field. (elifesciences.org)

The contribution of residue-solvent friction was accounted for using the Zimm model including internal friction (ZIF). (lu.se)

Such interaction happens when the RBD undergoes large conformational changes from the closed conformation to the open conformation. (sfbi.fr)

Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse -turn-type of conformation that is characterised by conformational angles of -70° and +70° around the X residue, and a C[stack i+1 ]H-Ni+2H interproton distance of 2.5 Å. (iisc.ac.in)

In this paper, we extend the model to support base pairs construction among k DNA sequences, which plays an essential role in realizing branch migrations. (elsevierpure.com)
The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. (lu.se)

Based on these data a model for the function of magnesium chelatase is proposed. (lu.se)

However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. (muni.cz)
Using spatial and population mobility models to inform outbreak response approaches in the Ebola affected area, Democratic Republic of the Congo, 2018-2020. (cdc.gov)

One-half of the domain swapped BTK structure represents the current model for autoinhibited BTK and closely resembles the compact structure of autoinhibited SRC kinases ( Fig. 1b ). (elifesciences.org)

ATP hydrolysis and the subsequent release of ADP from the NTD initiate a conformational return to the native apo open state and client release. (nature.com)

Conformer generation is useful in many aspects of both molecular modeling in general and drug discovery in particular. (schrodinger.com)

To achieve this objective, the candidate will develop a deep learning model to predict communication pathways. (loria.fr)

Machine learning for yield prediction for chemical reactions using in situ sensors JOURNAL OF MOLECULAR GRAPHICS & MODELLING. (nottingham.ac.uk)

Anatomy4

Organisms10

Chemicals and Drugs106

Analytical, Diagnostic and Therapeutic Techniques and Equipment50

Phenomena and Processes86

Disciplines and Occupations9

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Information Science8

Health Care2

Characterizing conformational changes1

Simulations11

Dynamics17

Protein15

Ligand3

Computational1

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Residues5

Theoretical2

Polyelectrolytes1

Spectroscopy5

Ensembles2

Nucleotide2

Undergo1

Investigating1

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Change4

Variability1

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Complexes1

Analysis3

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Molecules1

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