生物大分子
Designing functional protein sequences that satisfy multiple desired properties is a core research focus of protein engineering. Prior methods struggle with inability or inefficiency when dealing with numerous, often conflicting,…
We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges…
Antivirals are uniquely positioned to be deployed quickly during a new outbreak, especially when repurposed from approved drugs. Yet there are no FDA-approved antivirals for the majority of viral families with pandemic potential. Here we…
Scoring functions remain the principal bottleneck in molecular docking: they routinely fail to rank near-native poses above decoys, and their composite single-score design obscures the physicochemical basis of each ranking error. We present…
The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold…
Robust and efficient interpretation of QSAR methods is quite useful to validate AI prediction rationales with subjective opinion (chemist or biologist expertise), understand sophisticated chemical or biological process mechanisms, and…
Salts are an integral part of the environment for living systems and, therefore, understanding their effects on proteins and other biomolecules is of fundamental interest. Small-angle X-ray scattering (SAXS) of protein solutions can provide…
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances…
Computational molecular design requires binding arrangements that are not only energetically favorable but also chemically realizable. However, computational methods remain limited in directly recovering fragment pose pairs that can later…
Peptide self-assembly prediction offers a powerful bottom-up strategy for designing biocompatible, low-toxicity materials for large-scale synthesis in a broad range of biomedical and energy applications. However, screening the vast sequence…
Models from the AlphaFold (AF) family reliably predict one dominant conformation for most well-ordered proteins but struggle to capture biologically relevant alternate states. Several efforts have focused on eliciting greater conformational…
The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in their multiple sequence alignment would…
Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than…
Molecular docking is an essential step in the drug discovery process involving the detection of three-dimensional poses of a ligand inside the active site of the protein. In this paper, we address the Molecular Docking search phase by…
Generative models can now propose thousands of \emph{de novo} antibody sequences, yet translating these designs into viable therapeutics remains constrained by the cost of biophysical characterization. Here we present CrossAbSense, a…
During the formation of a thrombus, the architecture of the growing platelet aggregate is heterogeneous, with areas of dense and loosely packed platelets. The surface of activated platelets facilitate biochemical coagulation reactions that…
Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…
A method that reconstructs protein residue networks using suitable node selection and edge recovery policies produced numerical observations that correlate strongly (Pearson's correlation coefficient < -0.83) with published folding rates…