G. Gupta

Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape

Prediction of Conformational Ensembles and Structural Effects of State-Switching Allosteric Mutants in the Protein Kinases Using Comparative Analysis of AlphaFold2 Adaptations with Sequence Masking and Shallow Subsampling

This study adapts AlphaFold2 to predict conformational ensembles of allosteric ABL kinase mutants, showing that sequence masking and subsampling improve prediction of structural state shifts caused by mutations.

Host-derived Interleukin 1α induces an immunosuppressive tumor microenvironment via regulating monocyte-to-macrophage differentiation

This study shows that host-derived IL-1α promotes an immunosuppressive tumor microenvironment by regulating monocyte-to-macrophage differentiation in breast cancer.

Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations

This study uses AlphaFold2 and molecular dynamics to predict conformational ensembles and binding mechanisms of SARS-CoV-2 Omicron variants, showing agreement with experimental data.

Damage sensing through TLR9 Regulates Inflammatory and Antiviral Responses During Influenza Infection

This study shows that TLR9 sensing of tissue damage during influenza infection promotes inflammation and antiviral responses, but its absence leads to impaired viral clearance and prolonged lung injury.

Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling

This study adapts AlphaFold2 to predict conformational ensembles and allosteric states of ABL kinase using sequence scanning and frustration profiling, revealing limitations in detecting low-populated inactive states.

Preclinical Development of a Stabilized RH5 Virus-Like Particle Vaccine that Induces Improved Anti-Malarial Antibodies

This paper develops a stabilized RH5 VLP vaccine that induces improved anti-malarial antibodies compared to a soluble protein vaccine in preclinical studies.

AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance

This study uses AlphaFold2 and molecular simulations to analyze how mutations in SARS-CoV-2 Spike protein variants balance ACE2 binding and antibody resistance through epistatic interactions.

Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling

This study uses AlphaFold2 and molecular dynamics to analyze the structure, dynamics, and binding of SARS-CoV-2 Omicron BA.2.86 spike protein with ACE2 and antibodies, revealing key mutations that enhance immune evasion and ACE2 binding.

Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes

This study uses simulations and analysis of SARS-CoV-2 Omicron variants to examine conformational dynamics, protein stability, and evolution of cryptic binding pockets in the spike complex with ACE2.

Ensemble-Based Modeling of the SARS-CoV-2 Omicron BA.1 and BA.2 Spike Trimers and Systematic Characterization of Cryptic Binding Pockets in Distinct Functional States : Emergence of Conformation-Sensitive and Variant-Specific Allosteric Binding Sites

Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms

This study uses computational methods to analyze conformational dynamics and allosteric pockets in SARS-CoV-2 Omicron variants bound to ACE2, revealing how convergent mutations influence immune escape and functional mechanisms.

Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships

This study uses simulations and profiling to analyze how Omicron mutations affect binding, allostery, and thermodynamics in SARS-CoV-2 complexes with ACE2.

Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages : Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes

This study uses computational models to analyze how mutations in SARS-CoV-2 Omicron variants balance protein stability and ACE2 binding through epistatic interactions and dynamic changes.

Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants

This study compares the stability and adaptability of BA.1, BA.2, and BA.2.75 SARS-CoV-2 spike trimers using simulations and mutational analysis, finding BA.2.75 to be the most stable.

A Pre-transplant Blood-based Lipid Signature for Prediction of Antibody-mediated Rejection in Kidney Transplant Patients

This study identifies a lipid-based biomarker panel that predicts antibody-mediated rejection in kidney transplant patients with high accuracy.

Two Liberibacter Effectors Combine to Suppress Critical Innate Immune Defenses and Facilitate Huanglongbing Pathogenesis in Citrus

The paper investigates two CLas effectors, P235 and Effector 3, showing they suppress citrus innate immune responses and contribute to HLB pathogenesis by inhibiting immune proteins and inducing cell death.

Atomistic Simulations and Deep Mutational Scanning of Protein Stability and Binding Interactions in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms

Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating Variants

This study analyzes the functional effects of the D614G mutation in SARS-CoV-2 spike proteins using computational methods, revealing its role in enhancing infectivity through stability changes in residue interaction networks.

Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveal Allosteric Duality of Functionally Adaptable Hotspots

This study uses atomistic simulations and mutational scanning to analyze how different antibodies affect the allosteric properties of SARS-CoV-2 spike protein residues, revealing how mutations at K417, E484, and N501 influence antibody resistance.

What is the evidence available to support our knowledge about threats to the conservation of Galliformes in the Greater Himalaya?

This study reviews literature on threats to 24 Himalayan Galliformes species, finding poor evidence for most threats, with only one paper quantifying population impact.

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies : Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

This study identifies structurally adaptable allosteric hotspots in the SARS-CoV-2 spike protein that are targeted by mutations and antibodies, showing their role in modulating binding affinity and stability.

Computational Analysis of Protein Stability and Allosteric Interaction Networks in Distinct Conformational Forms of the SARS-CoV-2 Spike D614G Mutant: Reconciling Functional Mechanisms through Allosteric Model of Spike Regulation

This study uses computational methods to analyze how the D614G mutation in SARS-CoV-2 spike protein affects stability and allosteric communication, showing it enhances infectivity through structural changes.

The Long Pentraxin 3 (PTX3) Suppresses Immunity to Cutaneous Leishmaniasis by Negatively Regulating Th17 Response

This study shows PTX3 suppresses Th17 responses and increases susceptibility to Leishmania major infection by inhibiting IL-17A production and Th17-specific transcription factors.

Scaling up DNA data storage and randomaccess retrieval

This paper demonstrates large-scale DNA data storage with random access, storing 200MB of data in 13 million DNA oligonucleotides and achieving error-free retrieval.