# Protein Structure and Dynamics

**Type:** Topics  
**Canonical URL:** https://scholariq.org/topics/protein-structure-and-dynamics/

## Facts

| Field | Value |
| --- | --- |
| Description | This cluster of papers focuses on the prediction and analysis of protein structures using methods such as molecular dynamics simulations, force fields, homology modeling, and circular dichroism. It also explores topics related to intrinsically disordered proteins, enzyme catalysis, and the effects of macromolecular crowding on protein behavior. |
| Domain | Life Sciences |
| Field | Biochemistry, Genetics and Molecular Biology |
| OpenAlex ID | t10044 |
| Works | 80 |

## Topic papers all

Showing 15 of 80.

- [The Amber biomolecular simulation programs](https://scholariq.org/papers/the-amber-biomolecular-simulation-programs/)
- [A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations](https://scholariq.org/papers/a-point-charge-force-field-for-molecular-mechanics-simulations-of-proteins-based/)
- [AmberTools](https://scholariq.org/papers/ambertools/)
- [CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues](https://scholariq.org/papers/castp-computed-atlas-of-surface-topography-of-proteins-with-structural-and/)
- [Natural oligomers of the amyloid-β protein specifically disrupt cognitive function](https://scholariq.org/papers/natural-oligomers-of-the-amyloid-protein-specifically-disrupt-cognitive-function/)
- [ZDOCK: An initial‐stage protein‐docking algorithm](https://scholariq.org/papers/zdock-an-initial-stage-protein-docking-algorithm/)
- [Protein Data Bank: the single global archive for 3D macromolecular structure data](https://scholariq.org/papers/protein-data-bank-the-single-global-archive-for-3d-macromolecular-structure-data/)
- [Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles](https://scholariq.org/papers/lipid-bilayer-thickness-varies-linearly-with-acyl-chain-length-in-fluid/)
- [Recent Developments and Applications of the MMPBSA Method](https://scholariq.org/papers/recent-developments-and-applications-of-the-mmpbsa-method/)
- [Association between a specific apolipoprotein B mutation and familial defective apolipoprotein B-100.](https://scholariq.org/papers/association-between-a-specific-apolipoprotein-b-mutation-and-familial-defective/)
- [iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis](https://scholariq.org/papers/igemdock-a-graphical-environment-of-enhancing-gemdock-using-pharmacological/)
- [Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity](https://scholariq.org/papers/characterization-of-the-cytoplasm-of-escherichia-coli-k-12-as-a-function-of/)
- [Accelerated Poisson–Boltzmann calculations for static and dynamic systems](https://scholariq.org/papers/accelerated-poisson-boltzmann-calculations-for-static-and-dynamic-systems/)
- [Insight into the Mechanism of the Influenza A Proton Channel from a Structure in a Lipid Bilayer](https://scholariq.org/papers/insight-into-the-mechanism-of-the-influenza-a-proton-channel-from-a-structure-in/)
- [Structure of the Protein Phosphatase 2A Holoenzyme](https://scholariq.org/papers/structure-of-the-protein-phosphatase-2a-holoenzyme/)

## Topic primary papers

Showing 15 of 26.

- [The Amber biomolecular simulation programs](https://scholariq.org/papers/the-amber-biomolecular-simulation-programs/)
- [AmberTools](https://scholariq.org/papers/ambertools/)
- [Recent Developments and Applications of the MMPBSA Method](https://scholariq.org/papers/recent-developments-and-applications-of-the-mmpbsa-method/)
- [Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity](https://scholariq.org/papers/characterization-of-the-cytoplasm-of-escherichia-coli-k-12-as-a-function-of/)
- [Critical assessment of protein intrinsic disorder prediction](https://scholariq.org/papers/critical-assessment-of-protein-intrinsic-disorder-prediction/)
- [Mega-scale experimental analysis of protein folding stability in biology and design](https://scholariq.org/papers/mega-scale-experimental-analysis-of-protein-folding-stability-in-biology-and/)
- [DelPhi: a comprehensive suite for DelPhi software and associated resources](https://scholariq.org/papers/delphi-a-comprehensive-suite-for-delphi-software-and-associated-resources/)
- [RDOCK: Refinement of rigid‐body protein docking predictions](https://scholariq.org/papers/rdock-refinement-of-rigid-body-protein-docking-predictions/)
- [Alpha-helical, but not beta-sheet, propensity of proline is determined by peptide environment.](https://scholariq.org/papers/alpha-helical-but-not-beta-sheet-propensity-of-proline-is-determined-by-peptide/)
- [Enzymatic transition states and dynamic motion in barrier crossing](https://scholariq.org/papers/enzymatic-transition-states-and-dynamic-motion-in-barrier-crossing/)
- [Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis](https://scholariq.org/papers/calculating-protein-ligand-binding-affinities-with-mmpbsa-method-and-error/)
- [The IDP-Specific Force Field <i>ff14IDPSFF</i> Improves the Conformer Sampling of Intrinsically Disordered Proteins](https://scholariq.org/papers/the-idp-specific-force-field-i-ff14idpsff-i-improves-the-conformer-sampling-of/)
- [Virtual screening using molecular simulations](https://scholariq.org/papers/virtual-screening-using-molecular-simulations/)
- [New-Generation Amber United-Atom Force Field](https://scholariq.org/papers/new-generation-amber-united-atom-force-field/)
- [How Enzyme Dynamics Helps Catalyze a Reaction in Atomic Detail:  A Transition Path Sampling Study](https://scholariq.org/papers/how-enzyme-dynamics-helps-catalyze-a-reaction-in-atomic-detail-a-transition-path/)

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Source: ScholarIQ — public research metadata, principally OpenAlex. See https://scholariq.org/sources/ for provenance and https://scholariq.org/methodology/ for what these figures mean.