Models molecular. Medical search. Frequent questions

We invite contributions that focus on the use of computational tools (e.g., molecular dynamics, Monte Carlo, density functional theory) to study interfacial phenomena, including wetting, adsorption, and surfactants. (aiche.org)
The EJS Molecular Dynamics Exploration JavaScript Model shows the dynamics of simple atoms and molecules in a two-dimensional container. (compadre.org)
The Molecular Dynamics Exploration was developed by Wolfgang Christian at Davidson College using the Easy Java/JavaScript Simulation (EjsS) modeling and authoring tool created by Francisco Esquembre. (compadre.org)
The Molecular Dynamics Exploration packaged in an EPub 3 document. (compadre.org)
The Molecular Dynamics Exploration packaged as a stand alone Android app. (compadre.org)
This source code zip archive contains an XML representation of the Molecular Dynamics Exploration JavaScript Model. (compadre.org)
The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. (rcsb.org)
P. Palffy-Muhoray, T. Kosa and E. Weinan, Dynamics of a light driven molecular motor. (esaim-m2an.org)

Including corresponding data into 3D pharmacophore modeling is essential for efficient high throughput virtual screening. (acs.org)

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. (springer.com)
Computational molecular design has a great potential to promote enormous savings in time and cost in the discovery and development of functional molecules and assembles including drugs, dyes, solvents, polymers, and catalysis. (springer.com)

This approach enables correlation of tissue morphology and specific cell phenotypes with molecular images of tissue metabolism. (nih.gov)

By comparing simulation and experimental results, we validated our models and obtained insights. (lu.se)
By comparing simulation and experimental results, we validated our models and obtained insights into the mAbs' self-interaction properties, highlighting the role of both ion binding and charged patches on the mAb surfaces. (lu.se)

The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled. (wikipedia.org)
The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. (springer.com)
Appropriately weighted fuzzy pharmacophore models performed better in retrospective screening than similarity searching using only a single query molecule. (unboundmedicine.com)
Molecular modeling is the technique to determine the overall structure of an unknown molecule, be it a small one or a macromolecule. (bvsalud.org)

p21 and other tumor suppressor genes' inactivation are therefore most likely involved in the first steps of the cancer model, with later stages possibly involving protooncogene activation and inflammation. (medscape.com)
The overarching goal of understanding molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many tumor-inducing signaling proteins. (utoronto.ca)
In each model, tumor-bearing (TB) and control (CN) mice were injected with cancer cells and PBS, respectively. (spandidos-publications.com)
The directed expression of SV40 T antigen has led to the development of several important transgenic models with spontaneous epithelial tumor formation. (molvis.org)
This offers significant advantages for studying tumor pathogenesis and molecular mechanisms of oncogenesis caused by a single initiating oncogenic event introduced through the mouse germ line. (molvis.org)
A) We transferred molecular tumor subtype classifiers across four pairs of publicly available cancer datasets (bladder, breast, colorectal, pancreatic), covering 4,076 samples across 18 different tumor subtypes and three technological platforms (RNASeq, Affymetrix U133plus2, and HE1ST). (aacrjournals.org)

A molecular model is a physical model of an atomistic system that represents molecules and their processes. (wikipedia.org)
Molecular modeling has evolved from primitive models like hard spheres and square-wells to sophisticated descriptions of atomistic force laws, from the quantum scale to the mesoscale. (confex.com)
Atomistic models of the Spike proteins and the ACE2 receptor are available, with the glycan structures reduced to the first 1-2 sugar residues. (boku.ac.at)

They provide insight into structures and interactions at the molecular level, allowing researchers to understand, predict and manipulate characteristics and properties with greater clarity. (elsevier.com)
The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. (eyesopen.com)
The allosteric interactions and regulation of molecular chaperones and protein kinases allow for molecular communication and event coupling in signal transduction networks. (utoronto.ca)
Integration of computational systems biology and machine learning analysis of the Hsp90 interactions with oncogenic kinase mutants is then used to construct models of allosteric regulation of oncogenic proteins by molecular chaperones in signaling cascades. (utoronto.ca)
We will create computer models of Spike - ACE2 interactions with different variants of ACE2. (boku.ac.at)

Within the group, we develop and apply computational methods for multiscale molecular modeling and simulations, which are fully integrated with medicinal chemistry and structural/molecular biology. (iit.it)

There is a very wide range of approaches to physical modeling, including ball-and-stick models available for purchase commercially, to molecular models created using 3D printers. (wikipedia.org)
However, understanding possible approaches, selecting the most appropriate modelling technique for a given application, and accurately interpreting the results can be difficult without understanding the basic principles, benefits and challenges associated with each of the many available methods. (elsevier.com)
The series is designed first for graduate students and researchers predominantly in computational and theoretical chemistry as well as materials science and biomolecular science, who are seeking to use and understand molecular modelling methods and approaches for the first time. (elsevier.com)
Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. (nih.gov)
Network modelling and percolation analysis approaches were used to emulate thermal unfolding and characterize conformational landscapes of a wide range of protein kinases, revealing that chaperone dependency of protein kinase clients may be linked with the elevated conformational mobility of their inactive states induced by dynamic and energetic polarization of kinase lobes. (utoronto.ca)

We have studied the transgenic mouse strain, Tyrp-1-TAg, to try to gain insight into possible molecular mechanisms common to pigmented ocular neoplasms occurring spontaneously in the eyes of these mice and human choroidal melanoma. (molvis.org)
Using semi-quantitative reverse-transcription polymerase chain reaction (RT-PCR) and western blots experiments, we compared changes in ETS-1 and ETS-2 expression, their protein levels, and the regulation of some of their target gene expressions at different stages of the ocular tumoral progression in the transgenic mouse model, Tyrp-1-TAg, with those in normal eyes from control mice of the same age. (molvis.org)
Unlike cancer arising in the human population, tumors in genetically engineered mouse models arise in mice with well defined genetic backgrounds where genetic variability can be minimized. (molvis.org)
Objective: We assess the effects of drinking H2-water (water infused with H2) on oxidative stress model mice and subjects with MCI. (eurekaselect.com)
Methods: Transgenic mice expressing a dominant-negative form of aldehyde dehydrogenase 2 were used as a dementia model. (eurekaselect.com)
Molecular pathways of pulmonary inflammation following aspiration and inhalation of stainless steel welding fume in mice. (cdc.gov)

The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected. (wikipedia.org)
John Dalton represented compounds as aggregations of circular atoms, and although Johann Josef Loschmidt did not create physical models, his diagrams based on circles are two-dimensional analogues of later models. (wikipedia.org)
The concept of the chemical bond as a direct link between atoms can be modelled by linking balls (atoms) with sticks/rods (bonds). (wikipedia.org)

Some modeling analyses suggest 5 separate events are required in colon cancer. (medscape.com)
Molecular modelling analyses based on molecular mechanics, semi-empirical (PM3) and DFT (at B3LYP/6-31G* level) calculations show that MVC and its metabolites have large LUMO-HOMO energy differences ranging from 5.3 to 5.8 eV, indicating that the compounds would be kinetically inert. (scialert.net)
In this study, molecular modelling analyses have been carried out using the program Spartan 02 (Spartan, 2002) of MVC and its metabolites, with the aim of providing a better understanding of their toxicity. (scialert.net)
The results of biophysical and computational systems biology analyses combined with proteomics experiments have been integrated into a graph-based network model of allosteric regulation. (utoronto.ca)

Validation using an external test compound confirmed the high predictive ability of the model established (R-2: 0.990, RMSEP: 0.050). (uni-wuerzburg.de)
Funded by the Marie Skłodowska-Curie Actions programme, the ATM2BT project plans to create, test and validate a comprehensive and accurate predictive modelling framework to probe the inner workings of turbulence across all scales - from the nano to the macro world. (europa.eu)
We are bringing together a diverse world leading multidisciplinary team comprising of Japanese, USA and EU (AST, Queen Mary College, Aristotelio) Institutions in order to create a comprehensive, accurate and reliable predictive modelling framework to probe the inner secrets of turbulence. (europa.eu)

The multihit model postulates that several unique genetic mutations combine to cause cancer. (medscape.com)
Advances in genome resources and gene targeting have increased the attractiveness of the rat model for genetic studies but progress has been hampered by absence of relevant rat genome sequences. (europa.eu)

Tapping into both AlphaFold and RoseTTAFold, they tweaked the programs to predict which proteins are likely to tag-team and sketched up the resulting complexes into a 3D models. (singularityhub.com)

Unzip this archive in your Easy Java/JavaScript Simulations (EjsS) workspace to compile and run this model using EJS 5.2 or above. (compadre.org)
Simulations resulted in predictions for the internal fluxes, which describe at the molecular level how the organism lives and grows. (rsc.org)

However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models. (wikipedia.org)
The first molecular modeling software, developed at Columbia University in the mid-1960s by the late Cyrus Levinthal (see page 28), was capable of displaying and manipulating complex molecules in two dimensions. (the-scientist.com)
These packages can compute and illustrate the structure of molecules from any angle, perform quantum mechanical calculations, calculate a wide range of molecular properties, and identify structure-activity relationships. (the-scientist.com)
A variety of models with different degrees of fuzziness were calculated and tested for both classes of molecules. (unboundmedicine.com)
Molecular modelling analysis is now a mature discipline increasingly used to supply information about structures, relative stabilities and other properties of isolated molecules such as surface charge distribution, surface area, volume, heat of formation and dipole moment (Warren, 2003). (scialert.net)
The IEEE Transactions on NanoBioscience publishes basic and applied papers dealing both with engineering, physics, chemistry, modeling and computer science and with biology and medicine with respect to molecules, cells, tissues. (embs.org)

To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. (springer.com)
The molecular surfaces of all the compounds are found to abound in neutral regions so that they may be subject to lyophilic attacks. (scialert.net)
Molecular aspects of monooxygenases and bioactivation of toxic compounds. (cdc.gov)

Template self-replication 4 relies on binding of the precursors to the template by molecular recognition, usually combining a hydrogen bonding motif with size, shape and/or charge complementarity. (nature.com)
We previously reported that molecular hydrogen (H2) acts as a therapeutic and preventive antioxidant. (eurekaselect.com)

We have also analyzed mechanisms by which kinase drugs and allosteric Hsp90 modulators that may act synergistically and exert their pharmacological effect by depriving the client kinase of access to the molecular chaperone. (utoronto.ca)

Relating in vitro to in vivo exposures with physiologically based tissue dosimetry and tissue response models. (cdc.gov)

While histopathologists have not been prompt to adopt molecular diagnostics to date, the need to incorporate molecular pathology into the training of future histopathologists is imperative. (bmj.com)

A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. (nih.gov)
Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. (nih.gov)
PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. (nih.gov)
The ultimate goal is to develop universal modelling software that will describe the genesis and evolution of the complex phenomenon of turbulence. (europa.eu)
Our final goal will be to bring this framework of theoretical discoveries, represented in the form of a Unified nano-macro fluid flow accumulating state-of-the-art software, a Universal Modelling Software Tool (UMST), describing the genesis and evolution of turbulence from fundamental to scales, encountered in our everyday lives. (europa.eu)

Molecular graphics has made the visualization of molecular models on computer hardware easier, more accessible, and inexpensive, although physical models are widely used to enhance the tactile and visual message being portrayed. (wikipedia.org)
The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. (acs.org)

Molecular modelling methods are now indispensable tools in chemical, materials, and biomolecular sciences. (elsevier.com)
The Methods in Molecular and Materials Modelling series seeks to address this issue, providing detailed guidance on available methods and highlighting the pros and cons of different techniques within the context of specific research fields and application areas. (elsevier.com)
The Methods in Molecular and Materials Modelling series is a direct response to researcher feedback and seeks to combine foundational background information with practical, step-by-step guidance on the design, development, applications, and interpretation of molecular modelling methods in specific fields of interest. (elsevier.com)
Difference in library preparation methods and gene expression quantification platforms prevent the application of trained models to new data across labs. (aacrjournals.org)

Biophysical modeling of allosteric regulation in the protein kinases has offered additional insights into organizing principles of kinase activation by molecular chaperones that may be orchestrated by a cross-talk between key regulatory regions. (utoronto.ca)
Based on these findings, we developed a computational synthetic biology framework for design and re-engineering signal transduction networks and pathways that involve cross-talk between molecular chaperones and protein kinase clients. (utoronto.ca)
Our study offers a systems-based perspective on drug design and re-engineering of signaling networks by unravelling relationships between protein kinase networks with molecular chaperones and binding specificity of targeted kinase drugs. (utoronto.ca)

Network-defined modularity of interacting components and cross-talk in signal transduction networks are quantified through molecular mechanism of allosteric regulation. (utoronto.ca)
not unique for the embryonic system but are shared by other ogenesis regulation must consider different scales of multi-cellular modeling areas. (lu.se)

The great advances in cell and molecular biology which have accelerated our understanding of the pathogenesis of solid tumours have been embraced with variable degrees of enthusiasm by diverse medical professional specialties. (bmj.com)

It is our belief that this training will help to maintain in future the role of the pathologist at the centre of patient care as the integrator of clinical, morphological and molecular information. (bmj.com)

In support of this theory, the agent responsible for the TSE of cattle, called bovine spongiform encephalopathy (BSE), the accepted cause of variant Creutzfeldt-Jakob disease (vCJD) in humans ( 4 ), has been shown to be transmissible to at least 7 species ( 1 ), resulting in propagation of PrP d that retains the characteristic molecular signature of the original BSE prion strain ( 5 - 7 ). (cdc.gov)

Potential organizers of activities in areas of molecular biology, cell biology, network biology, immunology and systems biology are particularly encouraged to submit requests for support of Working Groups or Investigative Workshops. (bio.net)

After the development of X-ray crystallography as a tool for determining crystal structures, many laboratories built models based on spheres. (wikipedia.org)
In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. (springer.com)
the forward prediction is aimed at predicting physical, chemical and electric properties of a given molecular structure, and the backward prediction is to inversely identify appropriate molecular structures with the given desired properties. (springer.com)

Three fluorinated metformin derivatives (MTF1, MTF2 and MTF3) were synthesized and investigated for their human bloodstream - human serum albumin (HSA) interaction studies by multi-spectroscopic techniques (circular dichroism, steady state, time-resolved and synchronous fluorescence), combined with molecular docking and quantum chemical calculation. (amrita.edu)
We have created a complete model of the Spike-ACE2 interaction, with full glycosylation. (boku.ac.at)
The model confirms that the glycans can play a significant role in the interaction. (boku.ac.at)
Our models provide useful information about mAbs' self-interaction properties and can assist the screening of conditions driving to colloidal stability. (lu.se)

Rodent models offer significant advantages for analysis of disease phenotypes. (europa.eu)
These proposals provide a systematic route to elucidating the molecular and functional basis of disease phenotypes in SHR and WKY rats, and for translating these findings to advance understanding of common human diseases. (europa.eu)

Molecular Modeling Techniques and In-Silico Drug Discovery. (bvsalud.org)

Today, however, for less than a tenth of that cost, researchers can obtain molecular modeling software with high-resolution graphics. (the-scientist.com)
This in-person 5-day EMBO Workshop will gather early-career researchers and field leaders at the crossroads of single-cell omics, modelling and HPC to pave the way for realistic, scalable human digital twins of cells, tissues and organs. (bsc.es)
Many researchers worldwide have attempted to elucidate the molecular mechanism underlying muscle wasting using the two models ( 5 - 16 ). (spandidos-publications.com)

The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. (wikipedia.org)

This specialist training has two main goals: (1) to equip future practising histopathologists with basic knowledge of molecular diagnostics and (2) to create the option for those interested in a subspecialty experience in tissue molecular diagnostics to pursue this training. (bmj.com)

To define the histamine-binding site of this receptor, molecular modeling and site-directed mutagenesis were used to predict and alter amino acids residing in the histamine-binding pocket. (aspetjournals.org)

The Committee agreed that, despite the considerable progress that had been made in investigating variola virus, significant components of this research, most notably the refinement and use of an animal model developed in 2001 and the development of antiviral drugs, were unlikely to be completed by the end of 2002. (who.int)
Further, during extensive discussion about the potential availability of an animal model, additional research was identified that would necessitate access to live variola virus stocks after the expected 2002 destruction date. (who.int)

Symmetrical comparative modeling on fibrillar template is run through the RosettaCM protocol of Rosetta. (lu.se)

Finally, it attributed the highest importance to the power function value, the flow rate of the mobile phase, evaporation temperature, the content of the organic solvent in the mobile phase and the molecular descriptors such as molecular weight (MW), Radial Distribution Function-080/weighted by mass (RDF080m) and average coefficient of the last eigenvector from distance/detour matrix (Ve2_D/Dt). (uni-wuerzburg.de)

They are used increasingly together with experiment and a large and growing proportion of experimentally based studies make use of modelling techniques to help analyze and interpret data. (elsevier.com)

The symmetrical arrangement of closely packed spheres informed theories of molecular structure in the late 1800s, and many theories of crystallography and solid state inorganic structure used collections of equal and unequal spheres to simulate packing and predict structure. (wikipedia.org)

B) To demonstrate the transferability of prognostic models, we trained five Cox survival models on five target cancer datasets respectively (breast, lung, colorectal, liver, pancreatic) ranging from 186 to 2,919 RNASeq samples. (aacrjournals.org)

It integrates information from three-dimensional molecular alignments into correlation vector-based database screening. (unboundmedicine.com)

Using observations to deduce dust properties, grain-size distribution, and physical conditions in molecular clouds is a highly degenerate problem. (aanda.org)

If distinct conformers and glycotypes of PrP d are responsible for diversity of prion strains, then they would be expected to be able to impose these molecular characteristics onto PrP C of the same amino acid sequence (when transmitted or replicating within a species) and onto PrP C of a different primary sequence (when transmitted between species). (cdc.gov)
We have previously reported that the molecular characteristics, electrophoretic mobility, and glycoform ratio of the PrP res associated with the vCJD PrP d conformer were faithfully reproduced by PMCA ( 10 ). (cdc.gov)

An Example of a result obtained from a combination about modeling toolkits: conformers from Omega TK were overlayed using Shape TK while surfaces and coloring were generated by Spicoli TK. (eyesopen.com)

Best performance was obtained with pharmacophore models reflecting an intermediate degree of fuzziness, yielding an enrichment factor of up to 39 for the first 1% of the ranked database. (unboundmedicine.com)

Considering both experimental conditions and molecular descriptors, a mixed quantitative structure-property relationship (QSPR) The charged aerosol detector (CAD) is the latest representative of aerosol-based detectors that generate a response independent of the analytes' chemical structure. (uni-wuerzburg.de)
Considering both experimental conditions and molecular descriptors, a mixed quantitative structure-property relationship (QSPR) modeling was performed using Gradient Boosted Trees (GBT). (uni-wuerzburg.de)
Single cell experiments [ 11 ] could provide iterative validation of models with experimental results. (lu.se)

Here, we developed a multimodal imaging approach combining histopathology with mass spectrometry imaging (MSI) and same section imaging mass cytometry (IMC) to study the effects of Salmonella Typhimurium infection in the liver of a mouse model using the S. Typhimurium strains SL3261 and SL1344. (nih.gov)

Animal models of depression: Molecular perspectives. (bvsalud.org)

Molecular titanium( IV ) phenylhydroxamate complexes were synthesized as structural and spectroscopic models, and compared to functionalized TiO 2 nanoparticles. (rsc.org)

The discovery of the structure of DNA by Francis Crick and James Watson in the early 1950s ushered in a new era in molecular biologic science. (medscape.com)
You can make a model of the molecular structure of diamond using toothpicks and hard candies. (ehow.com)
Finally, we investigated the consequences of the model assumptions and the network structure on the quality of the flux predictions. (rsc.org)
Our goal is to create, within an existing 5-year histopathology training curriculum, the structure for formal substantial teaching of molecular diagnostics. (bmj.com)
The course covers theoretical models for the structure and reactions of atomic nuclear, as well as experiments in nuclear physics and their scientific applications. (lu.se)

Therefore, the present method is called the Bayesian molecular design. (springer.com)
Based on these models, to what extent can chemical engineers design molecular assemblies the way that civil engineers design bridges? (confex.com)

One hypothesis is that systems which are able to couple molecular-based template self-replication to cellular objects evolved, overcoming parasitism and problems of dilution, see Fig. 1 1 . (nature.com)
Previous studies have shown that xenobiotics and their metabolites which are kinetically labile and abound in electron-deficient regions on the molecular surface tend to induce cellular toxicity due to glutathione depletion and cause DNA damage due to oxidation of nucleobases in DNA (Huq, 2006a, b). (scialert.net)

The construction of physical models is often a creative act, and many bespoke examples have been carefully created in the workshops of science departments. (wikipedia.org)

The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. (nature.com)
Current thinking favors a seeded polymerization model for the conversion of PrP C into PrP d , which has led to the development of several cell-free in vitro conversion model systems ( 8 ). (cdc.gov)
This paper studies the problem of receiver modeling in molecular communication systems. (embs.org)

Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore be used to create new or extend existing functionality associated with those applications. (eyesopen.com)

Dynamics9

Corresponding data into 3D1

Computational molecular2

Metabolism1

Simulation2

Molecule4

Tumor6

Atomistic3

Interactions5

Multiscale1

Approaches5

Mice6

Atoms3

Analyses4

Predictive3

Genetic2

Proteins1

Simulations2

Molecules6

Compounds3

Hydrogen2

Mechanisms1

Vivo1

Pathology1

Evolution5

Visualization2

Methods4

Protein3

Regulation2

Pathogenesis1

Centre1

Humans1

Immunology1

Structures3

Interaction4

Phenotypes2

Drug Discovery1

Researchers3

Mathematical1

Tissue1

Receptor1

20022

Comparative1

Content1

Analyze1

Symmetrical1

Colorectal1

Correlation1

Properties1

Characteristics2

Surfaces1

Intermediate1

Experimental3

Infection1

Perspectives1

Structural1

Structure5

Design2

Cellular2

Science1

Systems3

Applications1