Quartz 4

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Dynamics

Created Sep 26, 2026Modified Sep 07, 2026

Conformational equilibria, flexibility, allostery, and their functional consequences.

39 items with this tag.

Sep 25, 2026
De novo designed binders can have unbound ensembles that differ from the bound state
Aug 19, 2026
Allostery can be mediated by changes in thermal fluctuations without a mean structural change
- biophysics/dynamics
Jul 17, 2026
Conformational entropy in antibodies decreases during affinity maturation
- antibodies/maturation
- biophysics/dynamics
Apr 28, 2026
Dynamics and specificity are inversely related
- biophysics/dynamics
- biophysics/interactions
Apr 21, 2026
Affinity-specificity tradeoff in antibodies is partially mediated by varying the magnitude of rigidification
Apr 21, 2026
Antibody-antigen binding modes are not necessarily defined by induced fit
- antibodies/recognition
- biophysics/dynamics
Apr 21, 2026
CDRH3 conformational rigidity reduces cross reactivity
Apr 21, 2026
Conformational entropy in antibodies is inversely proportional to antigen affinity
- antibodies/recognition
- biophysics/dynamics
Apr 21, 2026
Variable regions can adopt multiple interchain orientations, and these are difficult to predict
Apr 21, 2026
Beneficial mutations of enzymes far from active site improve substrate binding and product release
Apr 21, 2026
CDRH3 conformation is affected by interdomain orientation
- antibodies/architecture
- biophysics/dynamics
Apr 21, 2026
Conformationally stabilizing mutations can be identified from sequence clusters that are predicted to fold into that conformation when passed to AlphaFold2
Apr 21, 2026
Designed sequences of flexible proteins are dependent on conformation
- design/inverse-folding
- biophysics/dynamics
Apr 21, 2026
Epistasis in antibodies during affinity maturation can be driven by CDR rearrangements
Apr 21, 2026
Equilibrium dynamics of fold switching proteins change during evolution
- evolution/ancestry
- biophysics/dynamics
Apr 21, 2026
Evolutionary pathway between two folds identified using AlphaFold2 and ancestral sequence reconstruction
- evolution/ancestry
- biophysics/dynamics
Apr 21, 2026
Kappa subtype restricts CDRH3 dynamics
- antibodies/architecture
- biophysics/dynamics
Apr 21, 2026
Loops from one V-region chain affect the conformations and dynamics of loops in the other chain
- antibodies/architecture
- biophysics/dynamics
Apr 21, 2026
Nanobodies designed de novo from sequence are more flexible than either those designed from structure or those occurring in nature
Apr 21, 2026
PLM attention maps from specific heads can be used to predict allosteric networks
- model-analysis/interpretability
- biophysics/dynamics
Apr 21, 2026
Protein dynamics
- biophysics/dynamics
- biophysics/ensemble-analysis
Apr 21, 2026
Sodium- and proton-coupled transporters share a cation-independent ancestor
- evolution/ancestry
- biophysics/dynamics
Apr 21, 2026
Thermostable proteins have more small aliphatic amino acids that facilitate more flexible contacts
- biophysics/stability
- biophysics/dynamics
Apr 21, 2026
pLDDT and PAE inversely correlated with protein dynamics in dynamic naturally occurring proteins, but not de novo proteins
- prediction/confidence
- biophysics/dynamics
Apr 21, 2026
Arginine residues in CDRH3 increases promiscuity
Apr 21, 2026
Conformational dynamics facilitate the emergence of catalytic activity in non-enzyme ligand-binding proteins
Apr 21, 2026
Conformational entropy can decrease or increase following ligand binding
- biophysics/interactions
- biophysics/dynamics
Apr 21, 2026
Conformational sampling can smoothen fitness landscapes
- evolution/mutation-effects
- biophysics/dynamics
Apr 21, 2026
Eukaryotic viruses have more disordered proteins than prokaryotic viruses
- evolution/selection
- biophysics/dynamics
Apr 21, 2026
Fast dynamics of proteins drive slower conformational changes
- biophysics/dynamics
Apr 21, 2026
Lipid and detergent composition affects the conformational landscape of membrane proteins
- biophysics/dynamics
- evidence/measurements
Apr 21, 2026
Modifying conformational landscapes of proteins can give rise to new functions
- design/enzymes
- biophysics/dynamics
Apr 21, 2026
Mutation of allosteric residues can influence the equilibrium dynamics of designed proteins
- biophysics/dynamics
- design/backbones
Apr 21, 2026
Protein dynamics can be used as filtering criteria for the design of highly selective small molecules
Apr 21, 2026
Protein structure is more evolutionarily conserved than dynamics
- evolution/selection
- biophysics/dynamics
Apr 21, 2026
Rigidification of active site residues accelerates enzyme activity
Apr 21, 2026
The same protein can have two different structures across different organisms
- evolution/selection
- biophysics/dynamics
Apr 20, 2026
Fold-switching proteins
- biophysics/dynamics
- evolution/selection
Apr 17, 2026
Intrinsically disordered regions
- biophysics/dynamics

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