Sutanu Bhattacharya

Florida Polytechnic University · Computer Science

Protein contact maps have proven to be a valuable tool in the deep learning revolution of protein structure prediction, ushering in the recent breakthrough by AlphaFold2. However, self‐assessment of the quality of predicted structures are typically performed at the granularity of 3D coordinates as opposed to directly exploiting the rotation‐ and tr...

Motivation Protein contact maps have proven to be a valuable tool in the deep learning revolution of protein structure prediction, ushering in the recent breakthrough by AlphaFold2. However, self-assessment of the quality of predicted structures is typically performed at the granularity of 3D coordinates as opposed to directly exploiting the rotati...

Threading a query protein sequence onto a library of weakly homologous structural templates remains challenging, even when sequence-based predicted contact or distance information is used. Contact- or distance-assisted threading methods utilize only the spatial proximity of the interacting residue pairs for template selection and alignment, ignorin...

Sequence-based protein homology detection has emerged as one of the most sensitive and accurate approaches to protein structure prediction. Despite the success, homology detection remains very challenging for weakly homologous proteins with divergent evolutionary profile. Very recently, deep neural network architectures have shown promising progres...

Crystallography and NMR system (CNS) is currently a widely used method for fragment-free ab initio protein folding from inter-residue distance or contact maps. Despite its widespread use in protein structure prediction, CNS is a decade-old macromolecular structure determination system that was originally developed for solving macromolecular geometr...

Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to predict the correct folds for new proteins much more accurately than ever before. Despite the exciting progress, a...

Crystallography and NMR system (CNS) is currently the de facto standard for fragment-free ab initio protein folding from inter-residue distance or contact maps. Despite its widespread use in protein structure prediction, CNS is a decade-old macromolecular structure determination system that was originally developed for solving macromolecular geomet...

Motivation: Protein model quality estimation, in many ways, informs protein structure prediction. Despite their tight coupling, existing model quality estimation methods do not leverage inter-residue distance information or the latest technological breakthrough in deep learning that has recently revolutionized protein structure prediction. Result...

The development of improved threading algorithms for remote homology modeling is a critical step forward in template-based protein structure prediction. We have recently demonstrated the utility of contact information to boost protein threading by developing a new contact-assisted threading method. However, the nature and extent to which the qualit...

Recent advances in distance-based protein folding have led to a paradigm shift in protein structure prediction. Through sufficiently precise estimation of the inter-residue distance matrix for a protein sequence, it is now feasible to predict the correct folds for new proteins much more accurately than ever before. Despite the exciting progress, a...

Motivation Protein model quality estimation, in many ways, informs protein structure prediction. Despite their tight coupling, existing model quality estimation methods do not leverage inter-residue distance information or the latest technological breakthrough in deep learning that has recently revolutionized protein structure prediction. Results...

Motivation Threading a query protein sequence onto a library of weakly homologous structural templates remains challenging, even when sequence-based predicted contact or distance information is used. Contact- or distance-assisted threading methods utilize only the spatial proximity of the interacting residue pairs for template selection and alignme...

Protein threading is a powerful approach for predicting protein three-dimensional structure particularly when direct homologous relationships with known structures cannot be easily detected. However, remote homology detection via threading remains challenging, in part, due to the limitations of threading scoring function for selecting optimal struc...

Protein threading is a popular template-based approach for predicting protein three-dimensional structure in the absence of close templates. However, identifying remote homologous templates remains challenging. Inspired by recent progress in inter-residue contact prediction driven by sequence co-evolution and deep learning, we have developed a new...

Obverse Cover: The cover image is based on the Research Article Does inclusion of residue‐residue contact information boost protein threading? by Sutanu Bhattacharya, Debswapna Bhattacharya, DOI 10.1002/prot.25684.

Template‐based modeling is considered as one of the most successful approaches for protein structure prediction. However, reliably and accurately selecting optimal template proteins from a library of known protein structures having similar folds as the target protein and making correct alignments between the target sequence and the template structu...