Ab Initio Modeling
Ab Initio Modeling - Related Videos
06:37
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
0 Views •
Cited by 2 •
2021
Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).
12:11
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
0 Views •
Cited by 22 •
2020
The atmospheric concentrations of weakly bound molecular clusters can be computed from the thermochemical properties of low energy structures found through a multi-step configurational sampling methodology utilizing a genetic algorithm and semi-empirical and ab initio quantum chemistry.
10:27
Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
0 Views •
Cited by 2 •
2018
This protocol demonstrates how to obtain a low-resolution ab initio model and structural details of a detergent-solubilized membrane protein in solution using small-angle neutron scattering with contrast-matching of the detergent.
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
0 Views •
Cited by 10 •
2010
The crown region of different V3 loop sequences of the surface envelope glycoprotein (gp120) of HIV-1 can be structurally characterized in many cases by in silico folding of positions 10 to 22 of the loop using a state-of-the-art ab initio folding algorithm. Here we demonstrate the folding and evaluation of this region of the V3 loop from the R2 strain of HIV-1, a uniquely neutralization sensitive strain with puzzling functional properties.
12:31
In Vivo Modeling of the Morbid Human Genome using Danio rerio
0 Views •
Cited by 66 •
2013
Here, we present a systematic approach for developing physiologically relevant, sensitive and specific in vivo assays for interpreting variation in human pathology. Transient genetic manipulation via microinjection of WT and mutant human mRNA and morpholino (MO) antisense oligonucleotides harness the tractability of the developing zebrafish embryo to rapidly assay pathogenic mutations, especially, but not exclusively, in the context of human developmental disorders.
FAQs
The calculation approximates the electronic structure by solving a form of the Schrödinger equation. From the resulting description of electrons and nuclei, it can estimate molecular energies, geometries, charge distributions, and related properties. These outputs allow researchers to connect atomic arrangement with biochemical behavior without treating experimentally fitted parameters as the primary source of the prediction.
Nuclei and electrons provide the fundamental molecular inputs used to estimate electronic structure. Their calculated arrangement and distribution determine properties such as energy, geometry, and charge. Examining these quantities helps researchers compare alternative molecular conformations and assess how changes in atomic structure may influence the behavior or reactivity of a biochemical system.
The computational cost can make direct calculations difficult to apply routinely to very large biomolecules. This limitation affects how broadly the approach can be used across complex biochemical systems, even when atomic-resolution information would be valuable. Advances in algorithms and hybrid methods are helping extend its practical reach beyond smaller or more focused molecular regions.
A typical workflow begins by representing the relevant nuclei and electrons, then estimating the electronic structure through an approximation to the Schrödinger equation. Researchers use the resulting calculations to obtain energies, geometries, charge distributions, or related properties. They can then compare conformations, characterize an active site, or examine possible reaction intermediates.
Calculations can characterize the atomic structure and electronic properties of an enzyme active site, then examine how those features change across conformations or along a reaction mechanism. Comparing calculated energies, geometries, and charge distributions can help researchers investigate intermediates and relate active-site structure to chemical reactivity within the biochemical system.
It is useful when experiments require an atomic-level explanation of how molecular structure influences reactivity. Calculated geometries, energies, charge distributions, and related properties can provide a framework for comparing conformations or examining proposed intermediates. The results support interpretation of experimental observations, while computational cost remains an important consideration for very large biomolecules.