Full-Privacy Secured Search Engine Empowered by Efficient Genome-Mapping Algorithms.

Since the 90s, keyword-based search engines have been the only option for people to locate relevant web content through a simple query comprising one to a few keywords. These engines, whether free or paid, retained users' search queries and preferences, often to deliver targeted ads. Additionally, user-uploaded articles for plagiarism detection can further be stored as part of service providers' expanding databases for profit.

LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction.

Proteins perform many essential functions in biological systems and can be successfully developed as bio-therapeutics. It is invaluable to be able to predict their properties based on a proposed sequence and structure. In this study, we developed a novel generalizable deep learning framework, LM-GVP, composed of a protein Language Model (LM) and Graph Neural Network (GNN) to leverage information from both 1D amino acid sequences and 3D structures of proteins.

Helical structure motifs made searchable for functional peptide design.

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided.

DESP: Deep Enhanced Sampling of Proteins' Conformation Spaces Using AI-Inspired Biasing Forces.

The molecular structures (i.e., conformation spaces, CS) of bio-macromolecules and the dynamics that molecules exhibit are crucial to the understanding of the basis of many diseases and in the continuous attempts to retarget known drugs/medications, improve the efficacy of existing drugs, or develop novel drugs.

In Silico Study Reveals How E64 Approaches, Binds to, and Inhibits Falcipain-2 of Plasmodium falciparum that Causes Malaria in Humans.

Plasmodium falciparum malaria, which degrades haemoglobin through falcipain-2 (FP2), is a serious disease killing 445 thousand people annually. Since the P. falciparum's survival in humans depends on its ability to degrade human's haemoglobin, stoppage or hindrance of FP2 has antimalarial effects.

Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting.

Motivation: Programmed ribosomal frameshifting (PRF) is widely used by viruses and bacteria to produce different proteins from a single mRNA template. How steric hindrance of a PRF-stimulatory mRNA structure transiently modifies the conformational dynamics of the ribosome, and thereby allows tRNA slippage, remains elusive.

Results: Here, we leverage linear response theories and resolution-exchanged simulations to construct a structural/dynamics model that connects and rationalizes existing structural, single-molecule and mutagenesis data by resolution-exchanged structural modelling and simulations.

The Impairment of TorsinA's Binding to and Interactions With Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia.

Primary dystonia's prolonged muscle contractions and the associated abnormal postures and twisting movements remain incurable. Genetic mutation/deletion of GAG from TorsonA's gene resulting in ΔE303 (which weakens the binding between TorsinA and its activator, such as LULL1) primarily cause this neurodegenerative disorder. We studied TorsinA-LULL1 (or TorsinAΔE303-LULL1) bindings and interactions.

Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity.

Receptor-binding and subsequent signal-activation of interleukin-1 beta (IL-1β) are essential to immune and proinflammatory responses. We mutated 12 residues to identify sites important for biological activity and/or receptor binding. Four of these mutants with mutations in loop 9 (T117A, E118K, E118A, E118R) displayed significantly reduced biological activity.

Lycopersicon esculentum (Tomato) Prevents Adverse Effects of Lead on Blood Constituents.

Background: Lead is known for its adverse effects on various organs and systems. In this study, the ability of lead to adversely affect blood parameters was investigated, and Lycopersicon esculentum, or commonly known as tomato (a source of antioxidants), was administered orally in the form of tomato paste (TP) to reduce the adverse effects of lead.

Methods: The study involved 56 Wistar rats divided equally into 4 groups of 14 rats each: Control, LA(G), TP(G), and LA+TP(G).

Tomato (Lycopersicon esculentum) prevents lead-induced testicular toxicity.

Background: Lead, an example of heavy metals, has, for decades, being known for its adverse effects on various body organs and systems such that their functions are compromised.

Aim: In the present study, the ability of lead to adversely affect the male reproductive system was investigated and tomato (Lycopersicon esculentum: Source of antioxidants) paste (TP) was administered orally to prevent the adverse effects of Pb.

Materials And Methods: Fifteen Sprague Dawley rats, randomised into three groups (n = 5), were used for this study.