Quartz 4

Tag: conformational-dynamics

General

1 item with this tag.

Apr 21, 2026
Residual connections smoothen the loss landscape of neural networks
- conformational-dynamics

Allostery

6 items with this tag.

Apr 28, 2026
Dynamics and specificity are inversely related
- conformational-dynamics/allostery
Apr 21, 2026
PLM attention maps from specific heads can be used to predict allosteric networks
- protein-language-models/representations
- conformational-dynamics/allostery
Apr 21, 2026
Conformational dynamics facilitate the emergence of catalytic activity in non-enzyme ligand-binding proteins
- conformational-dynamics/allostery
Apr 21, 2026
Conformational entropy can decrease or increase following ligand binding
- conformational-dynamics/allostery
Apr 21, 2026
Protein dynamics can be used as filtering criteria for the design of highly selective small molecules
- conformational-dynamics/allostery
Apr 21, 2026
Thermal fluctuation is sufficient to explain allosteric changes in local protein dynamics
- conformational-dynamics/allostery

Evolution

10 items with this tag.

Apr 21, 2026
Affinity-specificity tradeoff in antibodies is partially mediated by varying the magnitude of rigidification
Apr 21, 2026
Conformational entropy in antibodies decreases during affinity maturation
Apr 21, 2026
Equilibrium dynamics of fold switching proteins change during evolution
- conformational-dynamics/evolution
Apr 21, 2026
Smooth protein folding landscapes are the result of natural selection
- conformational-dynamics/evolution
Apr 21, 2026
Conformational sampling can smoothen fitness landscapes
- conformational-dynamics/evolution
Apr 21, 2026
Fitness landscape navigability is correlated with its kurtosis and the centeredness of its maximum
- conformational-dynamics/evolution
Apr 21, 2026
Modifying conformational landscapes of proteins can give rise to new functions
- evolution-and-natural-selection
- conformational-dynamics/evolution
Apr 21, 2026
Potts models and PSSMs can model fitness landscapes
- conformational-dynamics/evolution
Apr 21, 2026
Protein structure is more evolutionarily conserved than dynamics
- conformational-dynamics/evolution
Apr 21, 2026
The same protein can have two different structures across different organisms
- conformational-dynamics/evolution
- evolution-and-natural-selection

Experimental ensembles

5 items with this tag.

Apr 21, 2026
Structure ensemble prediction methods are unable to accurately model subtle conformational differences captured by X-ray crystallography
- conformational-dynamics/experimental-ensembles
Apr 21, 2026
The PDB already contains implicit information about conformational dynamics based on subtle differences in closely related structures
- conformational-dynamics/experimental-ensembles
Apr 21, 2026
Cooling samples for cryogenic crystallography or cryo-EM narrows the conformational ensemble
- conformational-dynamics/experimental-ensembles
Apr 21, 2026
X-ray density can capture alternate conformations of proteins and their ligands
- conformational-dynamics/experimental-ensembles
Apr 11, 2026
NMR ensembles are not thermodynamic ensembles
- conformational-dynamics/experimental-ensembles

Kinetics

6 items with this tag.

Apr 21, 2026
Proteins with greater folding stability have more intermediate partially unfolded states
Apr 21, 2026
Ribosomes penalize the unfolded states of proteins
Apr 21, 2026
Fast dynamics of proteins drive slower conformational changes
- conformational-dynamics/kinetics
Apr 21, 2026
Lipid and detergent composition affects the conformational landscape of membrane proteins
- conformational-dynamics/kinetics
Apr 21, 2026
Small energy barriers separate unfolded and folded states of small fast-folding proteins
Apr 21, 2026
Transition matrices between metastable states approximate a protein's kinetics when their lag time exceeds relaxation time
- conformational-dynamics/kinetics

Modeling

23 items with this tag.

Apr 21, 2026
AF2 RMSD to ground truth correlated with RMSD between conformations
- alphafold2
- conformational-dynamics/modeling
Apr 21, 2026
AlphaFold2 and RosettaFold sometimes produce different conformations
Apr 21, 2026
AlphaFold2 predicts Apo conformations with poorer RMSD than holo conformations
Apr 21, 2026
AlphaFold2 predicts ground states more often
Apr 21, 2026
AlphaFold3 performs comparably to AlphaFold2 when predicting multiple conformations of fold-switching proteins
Apr 21, 2026
AlphaFold3 universally predicts the active state of ligand-bound GPCRs, even when the ligand is an antagonist
Apr 21, 2026
Alternate conformations can be sampled by inverting AlphaFold2 and backpropagating along specific user-picked collective variables
Apr 21, 2026
Alternate conformations can be sampled with MSA-based structure prediction methods using custom PDB databases and subsampled MSAs
- structure-prediction/sampling
- conformational-dynamics/modeling
Apr 21, 2026
Conformationally stabilizing mutations can be identified from sequence clusters that are predicted to fold into that conformation when passed to AlphaFold2
- alphafold2
- conformational-dynamics/modeling
Apr 21, 2026
Protein folding neural networks can be combined with VAEs for conformational modeling
- structure-prediction/sampling
- conformational-dynamics/modeling
Apr 21, 2026
Protein structure prediction methods are unable to predict the energetics of a conformational landscape unless explicitly trained for that purpose
- structure-prediction/limitations
- conformational-dynamics/modeling
Apr 21, 2026
Structure prediction from conformational samplers tends to be worse than those from vanilla structure prediction methods
Apr 21, 2026
Structure prediction methods undersample the conformational space they find to be high-confidence
- structure-prediction/sampling
- conformational-dynamics/modeling
Apr 21, 2026
Structure prediction neural networks trained on the same structural dataset are likely to predict the same conformation
Apr 21, 2026
The AlphaFold and ESMFold databases can be mined for alternate conformations
Apr 21, 2026
pLDDT and PAE inversely correlated with protein dynamics in dynamic naturally occurring proteins, but not de novo proteins
Apr 21, 2026
pTM is less lenient than pLDDT toward structural novelty when predicting alternate conformations
Apr 21, 2026
Biomolecular diffusion models cannot reproduce the equilibrium dynamics of the simulations they are trained on
Apr 21, 2026
Conformational sampling by AlphaFold3-generation methods can be achieved by scaling the pair representation
Apr 21, 2026
Guidance potentials can be added to diffusion-based structure prediction for enhanced sampling of protein conformations
Apr 21, 2026
Masking ESMFold can sometimes sample alternate conformations
- structure-prediction/sampling
- conformational-dynamics/modeling
Apr 21, 2026
Mutation of allosteric residues can influence the equilibrium dynamics of designed proteins
- conformational-dynamics/modeling
Apr 21, 2026
The latent space of VAEs can encode the conformational landscape of dynamic proteins
- conformational-dynamics/modeling

Molecular dynamics

12 items with this tag.

Apr 21, 2026
Abs modeled using MD are better for featurization than those modeled using homology modeling
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
MD trajectories reproduce experimental dG values to within 1 kcal per mol
- conformational-dynamics/molecular-dynamics
- thermostability/prediction
Apr 21, 2026
NVE ensemble
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
NVT ensemble
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
Likelihood of predicted contacts by MSA transformer weakly correlate with dwell time in molecular dynamics simulations
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
Linear MD encoders outperform nonlinear encoders when extrapolating to unseen regions of protein conformational space
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
MD force fields can be screened for agreement with experimental data
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
MD potentials from ML are more effective when protein-specific
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
Machine learning force fields for molecular dynamics require prior potentials
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
Mathematical terms in MD
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
Molecular dynamics simulation of an entire cell
- conformational-dynamics/molecular-dynamics
Apr 21, 2026
NPT ensemble
- conformational-dynamics/molecular-dynamics

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