SimulationComputationalMoleculeTumorProteinsAtomsInteractionsMechanismsAbstractRegulationGeneticDynamicsBiologyEvolutionMathematicalCOMPOUNDSAtomisticApproachesColorectalEpithelialMechanismStructuresCorrelationIntermediateProteinMoleculesComplexesFunctionalInteractionPropertiesExperimentsProcessesExtentMethodsSystemsSignificant advantagesSpheresResearchLungPhysicalComplexResultsScienceStatisticalVastBridgesDevelopmentCommunicationParametersEventsPresentLifeFieldWeightStudiesInflammation
Simulation3
- 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)
- 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)
Computational5
- 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)
- 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)
- 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)
- 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)
Molecule3
- 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)
Tumor6
- 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)
Proteins2
- 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)
- 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)
Atoms4
- 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)
- The EJS Molecular Dynamics Exploration JavaScript Model shows the dynamics of simple atoms and molecules in a two-dimensional container. (compadre.org)
Interactions2
- The allosteric interactions and regulation of molecular chaperones and protein kinases allow for molecular communication and event coupling in signal transduction networks. (utoronto.ca)
- We will create computer models of Spike - ACE2 interactions with different variants of ACE2. (boku.ac.at)
Mechanisms2
- 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)
- 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)
Abstract1
- We discuss the use of high-end rendering techniques to greatly increase the level of detail and interactivity of molecular visualisation, and describe the requirements placed upon that visualisation by the relationship between the abstract and physical models. (eg.org)
Regulation4
- 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)
- Network-defined modularity of interacting components and cross-talk in signal transduction networks are quantified through molecular mechanism of allosteric regulation. (utoronto.ca)
- 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)
- not unique for the embryonic system but are shared by other ogenesis regulation must consider different scales of multi-cellular modeling areas. (lu.se)
Genetic3
- 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)
- The multihit model postulates that several unique genetic mutations combine to cause cancer. (medscape.com)
- 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)
Dynamics4
- 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 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)
Biology1
- 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)
Evolution3
- 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)
Mathematical1
- 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)
COMPOUNDS2
- 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)
- Molecular aspects of monooxygenases and bioactivation of toxic compounds. (cdc.gov)
Atomistic2
- 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)
Approaches3
- 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)
- 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)
Colorectal1
- 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)
Epithelial1
- Modeling the influence of carbon nanotube and nanofiber physicochemical properties on key molecular initiating events and functional endpoints using epithelial, macrophage, and fibroblast cell models. (cdc.gov)
Mechanism1
- Many researchers worldwide have attempted to elucidate the molecular mechanism underlying muscle wasting using the two models ( 5 - 16 ). (spandidos-publications.com)
Structures3
- 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)
Correlation2
- It integrates information from three-dimensional molecular alignments into correlation vector-based database screening. (unboundmedicine.com)
- Review and update of ultrasonic vocalization in animals: Correlation with autism spectrum disorder experimental models? (bvsalud.org)
Intermediate1
- 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)
Protein2
- 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)
- water 1H relaxation dispersion profiles to be reported from empirical fitting procedures, the model-free approach is based on protein solutions ( 6 - 8 ), however, extended over a much wider rigorous theory and produces parameters with well-defined phys- frequency range than a Lorentzian dispersion (see Fig. 1). (lu.se)
Molecules2
- However, most molecules require holes at other angles and specialist companies manufacture kits and bespoke models. (wikipedia.org)
- A variety of models with different degrees of fuzziness were calculated and tested for both classes of molecules. (unboundmedicine.com)
Complexes1
- Molecular titanium( IV ) phenylhydroxamate complexes were synthesized as structural and spectroscopic models, and compared to functionalized TiO 2 nanoparticles. (rsc.org)
Functional2
- 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)
- We used 7 multiwalled carbon nanotubes and 2 carbon nanofibers (CNT/F) from U.S facilities to evaluate predictability, sensitivity, and the relationship of physicochemical characteristics to key molecular initiating events and functional responses following exposure. (cdc.gov)
Interaction3
- 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)
Properties1
- Using observations to deduce dust properties, grain-size distribution, and physical conditions in molecular clouds is a highly degenerate problem. (aanda.org)
Experiments1
- Single cell experiments [ 11 ] could provide iterative validation of models with experimental results. (lu.se)
Processes1
- The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. (nih.gov)
Extent3
- To what extent have these models impacted chemical engineering practice? (confex.com)
- Based on these models, to what extent can chemical engineers design molecular assemblies the way that civil engineers design bridges? (confex.com)
- The goal is to investigate to what extent grain growth (at constant dust mass) inside molecular clouds is able to explain the coreshine observations. (aanda.org)
Methods2
- The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. (nih.gov)
- Difference in library preparation methods and gene expression quantification platforms prevent the application of trained models to new data across labs. (aacrjournals.org)
Systems4
- The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. (nature.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)
- This paper studies the problem of receiver modeling in molecular communication systems. (embs.org)
- Additionally, the predictability of in vitro model systems to in vivo outcomes from a complementary study was determined. (cdc.gov)
Significant advantages1
- Rodent models offer significant advantages for analysis of disease phenotypes. (europa.eu)
Spheres2
- 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)
- The pharmacophore model is represented by a number of spheres of Gaussian-distributed feature densities. (unboundmedicine.com)
Research2
- 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)
Lung1
- In the present study, we established models of ECC and late cancer cachexia (LCC) and compared different stages of cancer cachexia using two cancer cachectic mouse models induced by colon-26 (C26) adenocarcinoma or Lewis lung carcinoma (LLC). (spandidos-publications.com)
Physical3
- 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)
- 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)
- August Wilhelm von Hofmann is credited with the first physical molecular model around 1860. (wikipedia.org)
Complex1
- The process may be straightforward and specific, as in the minimal template self-replicator model or more complex, as is the case for the replication of DNA. (nature.com)
Results1
- These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low-energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. (rcsb.org)
Science1
- 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)
Statistical1
- SpinAdapt transferred diagnostic and prognostic models over 14 cancer datasets covering 7,146 samples across six different cancer types and various platforms (RNASeq, microarray), while maintaining model accuracy and statistical significance. (aacrjournals.org)
Vast1
- The vast majority of water 1H disper- about molecular motions that can be derived from nuclear spin sions have been analyzed by an empirical 3-parameter function relaxation rates is contained in the spectral density function ( 1 ). (lu.se)
Bridges1
- This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission. (nature.com)
Development3
- With the development of plastic or polystyrene balls it is now easy to create such models. (wikipedia.org)
- A reasonable model is based on colon cancer development. (medscape.com)
- Although the exact process has not been elucidated, the sum of these mutations is believed to lead to cancer development in this model. (medscape.com)
Communication2
- We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. (embs.org)
- The object of our study aimed to review and to correlate genes involved in ASD and those related to ultrasonic communication in animal model studies of language-based social behavior at the PubMed database. (bvsalud.org)
Parameters1
- We built a grid of dust models and investigated the key parameters to reproduce the general trend of surface brightnesses and intensity ratios of both coreshine and near-infrared observations with the help of a 3D Monte Carlo radiative transfer code. (aanda.org)
Events2
- Some modeling analyses suggest 5 separate events are required in colon cancer. (medscape.com)
- However, which mutations are most important, which events must occur, and if a specific order is involved in molecular tumorigenesis is unclear. (medscape.com)
Present1
- This session will address these questions by surveying the models of past, present, and future with an invited panel of experts. (confex.com)
Life1
- Such 'model protocells' would allow the idea that life on earth emerged from a minimal self-organised cell-like entity-a protocell, to be tested experimentally 2 . (nature.com)
Field2
- 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)
- Normal interstellar radiation-field conditions are sufficient to find suitable grain models at all wavelengths for starless cores. (aanda.org)
Weight1
- Thus far, studies on muscle wasting using cancer cachectic models have generally focused on early cancer cachexia (ECC), before severe body weight loss occurs. (spandidos-publications.com)
Studies2
- To date, for both practical and ethical reasons, studies on muscle wasting have mainly depended on the use of murine models. (spandidos-publications.com)
- Regarding animal models in ASD, many studies focus on gene expression, cortical neuronal migration and cell maturation, and neural network deficits. (bvsalud.org)
Inflammation1
- The CNT/F represent a good model as they are known to induce cytotoxicity, inflammation, pathology, and genotoxicity. (cdc.gov)