Molecular Modeling
Molecular Modeling - Related Videos
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Molecular Models
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2020
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules. Skeletal Model Simpler two-dimensional representations of chemical compounds are accomplished using skeletal models. The illustration shows only the molecular framework or bonds without explicitly showing the atoms. In this representation, many of the carbon atoms...
05:56
Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
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Cited by 1 •
2022
The present protocol uses a biomolecular simulation package and describes the molecular dynamics (MD) approach for modeling the wild-type caspase and its mutant forms. The MD method allows for assessing the dynamic evolution of the caspase structure and the potential effect of mutations or post-translational modifications.
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MR Molecular Imaging of Prostate Cancer with a Small Molecular CLT1 Peptide Targeted Contrast Agent
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Cited by 3 •
2013
To demonstrate MR cancer molecular imaging with a small peptide targeted MRI contrast agent specific to clotted plasma proteins in tumor stroma in a mouse prostate cancer model.
12:02
Molecular Evolution of the Tre Recombinase
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Cited by 4 •
2008
Here we report the generation of Tre recombinase through directed, molecular evolution. Tre recombinase recognizes a pre-defined target sequence within the LTR sequences of the HIV-1 provirus, resulting in the excision and eradication of the provirus from infected human cells. While still in its infancy, directed molecular evolution will allow the creation of custom enzymes that will serve as tools of molecular surgery and molecular medicine.
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Molecular Orbital (MO) Theory
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2023
Source: Tamara M. Powers, Department of Chemistry, Texas A&M University This protocol serves as a guide in the synthesis of two metal complexes featuring the ligand 1,1'-bis(diphenylphosphino)ferrocene (dppf): M(dppf)Cl2, where M = Ni or Pd. While both of these transition metal complexes are 4-coordinate, they exhibit different geometries at the metal center. Using molecular orbital (MO) theory in conjunction with 1H NMR and Evans method, we will determine the geometry of these two...
FAQs
Molecular docking focuses on possible binding poses between molecules. Force-field calculations apply physical rules to atomic coordinates to estimate energetic changes, whereas molecular dynamics follows time-dependent movement. Used together, these approaches examine both a plausible interaction arrangement and how molecular motion may affect it, giving researchers complementary predictions rather than relying on a single computational view.
Atomic coordinates provide the spatial starting point for computational analysis. Force-field calculations use those coordinates to estimate energetic changes, while docking uses them to evaluate possible arrangements between interacting molecules. Molecular dynamics can then examine how those arrangements change over time. This connection between position, energy, and motion helps investigate recognition in antigen-antibody and host-pathogen systems.
A static structure may not capture how interacting molecules move over time. Molecular dynamics adds this time-dependent perspective, helping researchers investigate changes that could influence antigen-antibody recognition or interactions between pathogen proteins and host receptors. By considering movement as well as structure, modeling can generate hypotheses about biological interactions that may be missed when analysis uses only one molecular arrangement.
Researchers begin with atomic coordinates for the molecules of interest and select computational approaches suited to the question. Docking can propose binding poses, force-field calculations can estimate energetic changes, and molecular dynamics can examine movement over time. The resulting predictions help formulate testable hypotheses and prioritize experiments, rather than replacing experimental investigation.
It can characterize how antigens and antibodies may recognize one another, investigate interactions between pathogen proteins and host receptors, and help identify molecular features relevant to infection. These analyses may guide the selection of systems for closer study. In therapeutic or vaccine research, the structural insights can also support design efforts by linking candidate interactions to testable experimental questions.
Typical outputs include predicted binding poses, estimates of energetic changes, and descriptions of time-dependent molecular movements. Together, these results connect molecular structure with possible function and help researchers decide which interactions warrant experimental testing. They can also support prioritization of therapeutic compounds, pathogen proteins, host receptors, or vaccine-related molecular systems for further investigation.