• The multifaceted role of lncRNA MEG3 in kidney disease: a focus on mechanisms, therapeutic and diagnostic potential 

  Majumder, Syamantak; Gaikwad, Anil Bhanudas (Elsevier, 2025-09)

  Kidney disease represents a global health challenge, affecting millions of people and contributing to significant morbidity and mortality. Long noncoding RNAs are potentially emerging as regulators in cellular processes ...
• Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: Modeling studies of antibody and receptor binding 

  Basu, Sushmita (Elsevier, 2015-02)

  The envelope protein hemagglutinin (HA) of influenza viruses is primarily associated with host antibody and receptor interactions. The HA protein is known to maintain a functional balance with neuraminidase (NA), the other ...
• A structural perspective of RNA recognition by intrinsically disordered proteins 

  Basu, Sushmita (Springer, 2016-05)

  Protein-RNA recognition is essential for gene expression and its regulation, which is indispensable for the survival of the living organism at one hand, on the other hand, misregulation of this recognition may lead to their ...
• Effect of neighbouring residues in conformational plasticity of intrinsically disordered proteins 

  Basu, Sushmita (Elsevier, 2018-02)

  Effect of neighbouring residues in conformational plasticity of intrinsically disordered regions. The concept of unstructured proteins has opened new avenues in the field of structural biology. Intrinsically disordered ...
• Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins? 

  Basu, Sushmita (Elsevier, 2020-02)

  Intrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of ...
• Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method 

  Basu, Sushmita (Elsevier, 2021-05)

  Amyotrophic lateral sclerosis (ALS) and frontotemporal lobe degeneration (FTLD) are two inter-related intractable diseases of motor neuron degeneration. Fused in sarcoma (FUS) is found in cytoplasmic accumulation of ALS ...
• Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins 

  Basu, Sushmita (Wiley, 2021-10)

  Structure, function, and evolution are interdependent properties of proteins. Diversity of protein functions arising from structural variations is a potential driving force behind protein evolvability. Intrinsically ...
• Impaired nuclear transport induced by juvenile ALS causing P525L mutation in NLS domain of FUS: A molecular mechanistic study 

  Basu, Sushmita (Elsevier, 2022-04)

  Amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration (FTLD) are progressive neurological disorders affecting motor neurons. Cellular aggregates of fused in sarcoma (FUS) protein are found in cytoplasm ...
• qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids 

  Basu, Sushmita (Wiley, 2022-12)

  Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since ...
• Computational prediction of disordered binding regions 

  Basu, Sushmita (Elsevier, 2023)

  One of the key features of intrinsically disordered regions (IDRs) is their ability to interact with a broad range of partner molecules. Multiple types of interacting IDRs were identified including molecular recognition ...
• Real-time observation of macroscopic helical morphologies under optical microscope: a curious case of π–π stacking driven molecular self-assembly of an organic gelator devoid of hydrogen bonding 

  Basu, Sushmita (Wiley, 2022-12)

  Supramolecular assemblies such as tubules/helix/double helix/helical tape etc. are usually submicron objects preventing direct observation under optical microscope. Chiral-pure form of these assemblies is important for ...
• DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction 

  Basu, Sushmita (OUP, 2023-05)

  Intrinsic disorder in proteins is relatively abundant in nature and essential for a broad spectrum of cellular functions. While disorder can be accurately predicted from protein sequences, as it was empirically demonstrated ...
• CoMemMoRFPred: sequence-based prediction of MemMoRFs by combining predictors of intrinsic disorder, MoRFs and disordered lipid-binding regions 

  Basu, Sushmita (Elsevier, 2023-11)

  Molecular recognition features (MoRFs) are a commonly occurring type of intrinsically disordered regions (IDRs) that undergo disorder-to-order transition upon binding to partner molecules. We focus on recently characterized ...
• DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options 

  Basu, Sushmita (OUP, 2023-11)

  The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality ...
• HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins 

  Basu, Sushmita (OUP, 2023-12)

  Current predictors of DNA-binding residues (DBRs) from protein sequences belong to two distinct groups, those trained on binding annotations extracted from structured protein-DNA complexes (structure-trained) vs. intrinsically ...
• flDPnn2: accurate and fast predictor of intrinsic disorder in proteins 

  Basu, Sushmita (Elsevier, 2024-09)

  Prediction of the intrinsic disorder in protein sequences is an active research area, with well over 100 predictors that were released to date. These efforts are motivated by the functional importance and high levels of ...
• DescribePROT database of residue-level protein structure and function annotations 

  Basu, Sushmita (Springer, 2024-11)

  DescribePROT is a freely available online database of structural and functional descriptors of proteins at the amino acid level. It provides access to 13 diverse descriptors that include sequence conservation, putative ...
• Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses 

  Basu, Sushmita (Elsevier, 2024-12)

  Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. ...
• Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences 

  Basu, Sushmita (OUP, 2025-01)

  Computational prediction of nucleic acid-binding residues in protein sequences is an active field of research, with over 80 methods that were released in the past 2 decades. We identify and discuss 87 sequence-based ...
• pLMMoRF: A web server that accurately predicts membrane-interacting molecular recognition features by employing a protein language model 

  Basu, Sushmita (Elsevier, 2025-09)

  Interactions between proteins and lipids are crucial for numerous cellular processes. Some of the lipid interacting segments in protein sequences are intrinsically disordered regions (IDRs), which may gain secondary ...

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