A. Mondal

Protein Retrieval via Integrative Molecular Ensembles (PRIME) through extended similarity indices

PRIME improves identification of native-like protein structures from MD simulations by using extended similarity indices, achieving lower RMSD than traditional centroid-based methods.

Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein- Protein Binding Candidates in High-Throughput Protein Libraries

This paper introduces a computational pipeline using AlphaFold2 to prioritize protein-protein binding candidates from high-throughput libraries and identify binding epitopes.

G6PD deficiency mediated impairment of iNOS and lysosomal acidification affecting phagocytotic clearance in microglia in response to SARS-CoV-2

This study shows that G6PD deficiency in microglia impairs iNOS-mediated NO production and lysosomal acidification, leading to reduced phagocytosis of SARS-CoV-2 and increased COVID-19 severity.

Long-term cold selection leads to increased thermal plasticity of male body size and thermal canalization of fecundity in populations of Drosophila melanogaster

Development of covalent chemogenetic K2P channel activators

This paper develops a chemogenetic method to irreversibly activate K2P channels, enabling studies of their function and potential therapeutic applications.

MGDrivE 3: A decoupled vector-human framework for epidemiological simulation of mosquito genetic control tools and their surveillance

MGDrivE 3 simulates mosquito genetic control tools and their epidemiological impacts using a decoupled vector-human framework, incorporating detailed malaria transmission models and surveillance modules.

Eliminating Malaria Vectors with Precision Guided Sterile Males

This paper develops a precision guided Sterile Insect Technique (pgSIT) for malaria vector control using CRISPR to achieve high male sterility and female lethality in Anopheles gambiae.

Connexin 43 mediated collective cell migration is independent of Golgi orientation

This study shows that Connexin 43 promotes collective cell migration by reducing Golgi reorientation, independent of directed secretory trafficking.

GENERALIST: An efficient generative model for protein sequence families

The paper introduces GENERALIST, a generative model for protein sequence families that accurately captures amino acid covariation and predicts stable sequences.

Structural basis for CaVα2δ:gabapentin binding

This study presents the cryo-EM structure of a gabapentin-bound calcium channel, revealing the binding pocket and explaining isoform selectivity.

EMC holdase:CaV1.2/CaVβ3 complex and CaV1.2 channel structures reveal CaV assembly and drug binding mechanisms

The paper presents cryo-EM structures of CaV1.2 channels with auxiliary subunits and chaperones, revealing assembly mechanisms and drug binding sites.

Targeting an evolutionarily conserved "E-L-L" motif in the spike protein to develop a small molecule fusion inhibitor against SARS-CoV-2

This study identifies an evolutionarily conserved 'E-L-L' motif in the SARS-CoV-2 spike protein as a target for small molecule fusion inhibitors, showing posaconazole effectively blocks viral entry across variants.

Structure determination of protein-peptide complexes from NMR chemical shift data using MELD.

The paper develops a hybrid MELD-NMR approach to determine structures of flexible protein-polypeptide complexes using only NMR chemical shift data, achieving accurate results for ET domain-BET protein interactions.

A species-specific signature residue in the PB2 subunit of the bat influenza virus polymerase restricts viral RNA synthesis.

Preclinical validation of a second generation leishmanization vaccine against vector transmitted fatal visceral leishmaniasis

This study evaluates the protective efficacy of a CRISPR-edited Leishmania major strain against visceral leishmaniasis in hamsters and shows it induces a pro-inflammatory immune response and prevents disease.

Structure Specific Neuro-toxicity of α-Synuclein Oligomer

This study compares natural and induced α-synuclein oligomers, finding natural oligomers more toxic due to their helical structure and stability.

Mechanism of Dynamic Binding of Replication Protein A to ssDNA

This study investigates how RPA binds to ssDNA of different lengths using molecular simulations, revealing dynamic mechanisms that depend on ssDNA size.

Development of a copper-graphene nanocomposite based transparent coating with antiviral activity against influenza virus

This paper develops a copper-graphene nanocomposite transparent coating with antiviral activity against influenza virus, showing rapid inactivation of virions and reduced viral replication.

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

CryoFold determines protein structures from electron density maps using molecular dynamics and physical knowledge, producing ensembles of low-energy conformations validated experimentally.

Phosphorylation controls RNA binding and transcription by the influenza virus polymerase

This study identifies phosphorylation sites in the influenza virus polymerase that regulate its activity and virus replication by affecting RNA binding and transcription.

Microbially induced calcite precipitation using Bacillus velezensis with guar gum

This study investigates the efficiency of microbially induced calcite precipitation using Bacillus velezensis with guar gum as a biopolymer additive, showing significant precipitation and consolidation of sand.