Shruthi Viswanath

Evaluation of methods for AlphaFold-based integrative modeling

This study evaluates AlphaFold-based integrative modeling methods using chemical crosslinks, finding they often rely more on learned priors than input data.

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome

The paper builds structural models of HDAC1/2-containing chromatin remodeling complexes using XL-MS and integrative modeling, revealing how the CTD IDR of HDAC1 folds into alpha helices.

GATA3-extension mutants rewire lineage identity in luminal breast cancer

The paper shows that eGATA3 mutations alter transcriptional regulation and lineage identity in luminal breast cancer without losing DNA-binding function.

Integrative structure determination of a human mitochondrial contact site and cristae organizing system (MICOS) sub-assembly

The paper determines the structure of a MICOS sub-assembly using integrative methods, revealing novel interfaces and mutation hotspots.

Cell-autonomous Wnt activity promotes transient re-programming and cell cycle re-entry of coronary artery endothelial cells

The paper identifies Wnt signaling as essential for coronary artery endothelial cell reprogramming and collateral artery formation in mice, with implications for cardiovascular disease.

Disobind: a sequence-based, partner-dependent contact map and interface residue predictor for intrinsically disordered regions

Disobind predicts inter-protein contact maps and interface residues for intrinsically disordered regions using sequence-based deep learning, outperforming existing methods without requiring structures or alignments.

PickET: An unsupervised method for localizing macromolecules in cryo-electron tomograms

PickET localizes macromolecules in cryo-ET tomograms without expert annotations or prior structures, showing effectiveness across diverse datasets.

A new discrete-geometry approach for integrative docking of proteins using chemical crosslinks

This paper introduces wall-EASAL, a discrete geometry method for integrative protein docking using crosslinks, showing improved performance and efficiency over IMP.

StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures

StrIDR is a database of intrinsically disordered regions with experimentally resolved structures, providing insights into IDR dynamics and facilitating computational studies.

Optimizing representations for integrative structural modeling using Bayesian model selection

This paper introduces NestOR, a Bayesian method to automatically select optimal coarse-grained representations for integrative structural modeling, improving accuracy and efficiency.

PrISM: precision for integrative structural models

PrISM identifies high and low-precision regions in integrative models by accounting for varying input information.