For decades, the existence of the hydrophobic core, a region in the 3D structure of proteins where hydrophobic amino acids reside together, has been considered a general property in proteins. What we have found now may extend that model.
arXiv:2608. 16094v1 Announce Type: new Abstract: Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation.
arXiv:2605. 01625v3 Announce Type: replace Abstract: Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology.
arXiv:2606. 14737v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulations generate trajectories in a high-dimensional configuration space whose analysis critically depends on molecular descriptors, typically handcrafted observables or learned kinetic embeddings.
arXiv:2607. 16087v1 Announce Type: new Abstract: AlphaFold2's 93 million parameters, shaped by the evolutionary record of protein structure encoded in the Protein Data Bank and in sequence alignments, are conventionally treated only as machinery for converting sequence to structure.
arXiv:2602. 06020v3 Announce Type: replace Abstract: How do protein structure prediction models fold proteins?
arXiv:2606. 11651v1 Announce Type: new Abstract: Synthetic random heteropolymers (RHPs), consisting of a predefined set of monomers, offer an approach toward the design of protein-like materials.
arXiv:2606. 07567v1 Announce Type: cross Abstract: Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure.
arXiv:2606. 11243v1 Announce Type: new Abstract: De novo protein generation has transformative potential in therapeutic design, enzyme engineering, and synthetic biology.
arXiv:2607. 22143v1 Announce Type: new Abstract: Molecular glue degraders have emerged as a promising strategy for targeted protein degradation by inducing ternary complex formation between an E3 ubiquitin ligase and a target protein.
arXiv:2606. 05474v1 Announce Type: cross Abstract: Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs, a binder that engages both active and inactive states provides no functional specificity regardless of how tightly it binds.
arXiv:2606. 02048v1 Announce Type: new Abstract: We propose a novel computational toolbox that integrates Topological Data Analysis (TDA), Differential Box Counting (DBC), Multifractal Partition (MFP), and Local Binary Patterns (LBP), applied to time-lapse super-resolution STED microscopy images of sodium caseinate gelation induced by glucono-delta-lactone (GDL) at 30 {\deg}C and 40 {\deg}C and two GDL concentrations (1.
arXiv:2607. 15309v1 Announce Type: cross Abstract: Proteins function through coordinated motion across multiple spatial and temporal scales, underpinning processes such as ligand binding, allostery, and catalysis.