A. Srivastava

Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering

This study demonstrates that the REHT method efficiently samples membrane-bound conformations of the Osh4 ALPS peptide, revealing a preference for horizontal over vertical conformations.

SOP-MULTI: A self-organized polymer based coarse-grained model for multi-domain and intrinsically disordered proteins with conformation ensemble consistent with experimental scattering data

The paper introduces SOP-MULTI, a coarse-grained force field for simulating multi-domain and intrinsically disordered proteins, validated against experimental scattering data.

The atypical antipsychotic aripiprazole alters the outcome of disseminated Candida albicans infections.

This study shows that aripiprazole, an atypical antipsychotic, worsens outcomes of disseminated Candida albicans infections in mice but has minimal effects on fungal growth or gene expression.

Patient-derived tumor organoids from resected non-small cell lung cancers for high-throughput response testing with approved and repurposed drugs

This study develops patient-derived tumor organoids from non-metastatic NSCLC tumors to test drug responses and identify chemoresistance mechanisms, finding 50% of organoids were chemo-resistant and could be sensitized by repurposed drugs.

hnRNPA1 RGG-box acts a "catalyst" in UP1-induced destabilization of RNA and DNA telomeric G-Quadruplexes

This study investigates how the RGG-box of hnRNPA1 interacts with telomeric G-quadruplexes, showing it preferentially binds to specific structures and can destabilize them, aiding hnRNPA1-UP1 in telomere maintenance.

sAMP-VGG16: Drude polarizable force-field assisted image-based deep neural network prediction model for short antimicrobial peptides

This paper introduces an image-based deep neural network model for predicting antimicrobial peptides using Drude polarizable force-field atom types, achieving high accuracy and efficiency.

Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance

This study identifies Mtb genes involved in antibiotic tolerance under nutrient-starved conditions through a functional genome screen, revealing potential therapeutic targets.

HSP70 binds to specific non-coding RNA and regulates human RNA Polymerase III

This study identifies HSP70's interaction with non-coding RNA transcribed by RNA Polymerase III and shows its role in facilitating transcription of these RNAs.

Glycans modulate lipid binding in Lili-Mip lipocalin protein

This study investigates how glycans affect lipid binding in Lili-Mip lipocalin using molecular dynamics simulations and structural analysis.

Clustering conformational ensembles of intrinsically disordered proteins with t-distributed stochastic neighbor embedding

This paper uses t-SNE to cluster conformations of intrinsically disordered proteins, revealing structurally similar groups and insights into ligand binding mechanisms.

Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations

The paper ranks JAK2/STAT5 inhibitors based on kinetic properties using MMVT in SEEKR2 to explain their selectivity over JAK3.

Interplay of the folded domain and disordered low-complexity domains along with RNA sequence mediate efficient binding of FUS with RNA

This study uses molecular simulations to investigate how FUS's folded and disordered domains interact with RNA, revealing cooperative binding mechanisms and structural roles in RNA recognition.

Nascent-Chain Interaction Networks and Their Effect on the Bacterial Ribosome

This study identifies specific ribosomal protein interactions with nascent chains of foldable proteins and shows the ribosome provides unbiased support to RNCs regardless of sequence or foldability.

A multi-omics analysis of glioma chemoresistance using a hybrid microphysiological model of glioblastoma

This study uses a hybrid microphysiological model to analyze glioma chemoresistance and identifies molecular changes associated with resistance mechanisms.

Development and application of genetic ancestry reconstruction methods to study diversity of patient-derived models in the NCI PDXNet Consortium

The paper develops a genetic ancestry pipeline to assess diversity in PDX models and finds overrepresentation of European ancestry models, highlighting gaps in minority representation for cancer research.

Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor

The paper evaluates binding interactions of SARS-CoV-2 spike variants with hACE2 using ELISA and cellular models, finding that N501Y in RBD enhances binding efficiency, particularly distinguishing C.1.2 from Delta.

Using Packing Defects in Heterogeneous Biological Membrane as a Lens to Explore Protein Localization Propensity and Small Molecule Permeability

The paper uses computer simulations to study how membrane heterogeneity affects protein localization and small molecule permeability by analyzing packing defects and local membrane order.

Protein as evolvable functionally-constrained amorphous matter

The paper models proteins as amorphous materials using graph representations to study functional features and their evolutionary emergence.

Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies

This study edits the PRR-βE1 region in HSPCs to suppress HbA and enhance HbF production, showing therapeutic benefits for β-hemoglobinopathies.

A Genomically and Clinically Annotated Patient Derived Xenograft (PDX) Resource for Preclinical Research in Non-Small Cell Lung Cancer

The paper describes a collection of 79 genomically and clinically annotated lung cancer PDX models that retain patient tumor features and treatment responses, available through MMHCdb.

Identification of a novel interaction between Theileria Prohibitin (TaPHB-1) and bovine RUVBL-1

This study identifies a novel interaction between Theileria annulata prohibitin (TaPHB-1) and bovine RUVBL-1, revealing potential roles in host cell transformation and cancer-like phenotypes.

RET activation controlled by MAB21L4-CacyBP interaction drives squamous cell carcinoma

This study identifies RET activation driven by MAB21L4-CacyBP interaction as a driver of squamous cell carcinoma and shows RET inhibition as a potential therapeutic strategy.

Discovery of Potent Inhibitors of α-Synuclein Aggregation Using Structure-Based Iterative Learning

This paper uses structure-based machine learning to identify potent small molecule inhibitors of α-synuclein aggregation, achieving compounds two orders of magnitude more potent than previous reports.

PDXNet Portal: Patient-Derived Xenograft model, data, workflow, and tool discovery

The paper introduces the PDXNet Portal, a centralized resource for PDX models and data, offering analysis workflows and facilitating cancer research collaboration.

Membrane remodeling due to mixture of multiple curvature proteins

This study extends a mesoscopic membrane model to simulate how multiple curvature proteins interact to deform membranes, revealing how their mixtures influence vesicle morphology and cargo sorting.

Enthalpic and Entropic Contributions to Interleaflet Coupling Drive Domain Registration and Anti-registration in Biological Membrane

The paper develops an analytical theory to explain domain registration and anti-registration in biological membranes by analyzing enthalpic and entropic contributions to interleaflet coupling.

Regulation of distinct STAT3 dynamics in pro (IFNγ) and anti (IL-10) inflammatory pathways and in their cross-talk: insights from a data-driven model

The paper builds a data-driven model to analyze STAT3 dynamics in IFNγ and IL10 pathways and their cross-talk, identifying regulatory elements controlling their responses.

Comparative Transcriptome Profiling of High and Low oil yielding Santalum album L.

This study compares transcriptomes of high and low oil yielding Santalum album trees to identify genes involved in oil biosynthesis.

Evaluation of in vitro and in vivo toxicity of pristine molybdenum disulphide nanosheets in Swiss albino mice

This study evaluates the toxicity of molybdenum disulphide nanosheets in vitro and in vivo, finding no toxicity at lower concentrations but significant effects at higher doses.

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme

The paper introduces an efficient hybrid parallel tempering method to accurately sample conformational ensembles of metamorphic and intrinsically disordered proteins, matching experimental data without reweighting.