Mallur Srivatsan Madhusudhan

Chemical Proteomics Identifies Protein Ligands for Monoacylglycerol Lipids

The paper identifies protein ligands for monoacylglycerol lipids using chemical proteomics in mouse brain and cell lysates, revealing Hippocalcin as a novel ligand involved in calcium sensing.

Overhang Optimizer for Golden Gate Assembly (OOGGA)

OOGGA optimizes Golden Gate assembly overhangs for accuracy and efficiency, outperforming NEBridge SplitSet in fidelity and efficiency metrics.

Bioinformatics analysis identifies sequence determinants of enzymatic activity for the PHARC associated lipase ABHD12

The paper identifies sequence determinants of ABHD12 enzymatic activity through bioinformatics and biochemical validation, and identifies a Drosophila ortholog with lyso-PS lipase activity.

Motif distribution in genomes gives insights into gene clustering and co-regulation

The paper analyzes DNA motif distributions across genomes to uncover patterns related to gene clustering, co-regulation, and spatial organization.

High-affinity biomolecular interactions are modulated by low-affinity binders

This study shows low-affinity binders can modulate high-affinity interactions through herd regulation, impacting biological processes like sex determination and signaling thresholds.

COCONUT: An analysis of coiled-coil regions in proteins

The paper introduces COCONUT, a computational tool using machine learning to predict coiled-coil dimer orientation and model coiled-coil structures.

Prediction of SUMOylation targets in Drosophila melanogaster

The paper predicts SUMOylation targets in Drosophila melanogaster using sequence homology from human and mouse SUMOylation data, identifying motifs, protein families, and functional preferences.

3-D structure based prediction of SUMOylation sites

The paper introduces a 3-D structure-based method to predict SUMOylation sites with 81% accuracy and a Matthews Correlation Coefficient of 0.4.

A structural database of chain-chain and domain-domain interfaces of proteins

The paper creates a structural database of 178,465 protein-protein and domain-domain interfaces, revealing similarities between interactions and potential therapeutic applications.

JEDII: Juxtaposition Enabled DNA-binding Interface Identifier

JEDII predicts DNA-protein interaction residues, nucleotides, and amino acids by analyzing structural hydrogen-bonding interactions, achieving high accuracy in binding site prediction.

Packpred: Predicting the functional effect of missense mutations

Packpred predicts the functional effect of missense mutations using a statistical potential and substitution matrix, outperforming existing methods on multiple datasets.

Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures

The paper introduces MoDS, a score for assessing protein structure models using monolink data, and shows combining it with MNXL improves model scoring, supporting the use of monolink data in integrative structure determination.

Predicting and Designing therapeutics against the Nipah virus

This paper predicts and designs therapeutics against Nipah virus by modeling its proteins, identifying peptide and small molecule inhibitors, and analyzing viral strain sequences for drug resistance.

A knowledge-based scoring function to assess the stability of quaternary protein assemblies

This paper introduces PIZSA, a scoring function to assess protein-protein interaction stability, which outperforms existing methods in distinguishing native from non-native conformations.