Author

Nishita Mandal

International Institute of Molecular and Cell BiologyORCID 0000-0002-9114-0281Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 3

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Approach:mixed model· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Approach:simulation· 1

Frequent Co-Authors

Bartłomiej SurpetaiD· 3 shared Jan BrezovskýiD· 3 shared Aravind Selvaram ThirunavukarasuiD· 2 shared Carlos Eduardo Sequeiros-BorjaiD· 2 shared Adolfo B. PomaiD· 1 shared Cedrix J. Dongmo FoumthuimiD· 1 shared Dheeraj Kumar SarkariD· 1 shared Jan A. StevensiD· 1 shared

Activity by Year

2021-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersBioinformatics

Bartłomiej SurpetaORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Benchmarking coarse-grained simulation methods for investigation of transport tunnels in enzymes

Nishita Mandal, Jan A. Stevens, Adolfo B. Poma, Bartłomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Aravind Selvaram Thirunavukarasu, ‪Siewert J. Marrink, Jan Brezovský

This study benchmarks coarse-grained simulation methods for analyzing enzyme transport tunnels, finding they efficiently capture tunnel geometry but vary in replicating all-atom dynamics.

bioRxiv · Sep 16, 2024 · PreprintBioinformatics

Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics

Nishita Mandal, Bartłomiej Surpeta, Jan Brezovský

This study uses Gaussian accelerated MD simulations to improve tunnel sampling in enzymes, revealing new transient tunnels and their functional relevance.

Journal of Chemical Information and Modeling · Aug 15, 2024Peer-reviewedBioinformatics

TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them

Jan Brezovský, Aravind Selvaram Thirunavukarasu, Bartłomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Nishita Mandal, Dheeraj Kumar Sarkar, Cedrix J. Dongmo Foumthuim, Nikhil Agrawal

TransportTools enables efficient analysis of ligand transport pathways through voids in biomolecules using high-throughput molecular dynamics data.

Bioinformatics · Dec 28, 2021Peer-reviewedBioinformatics