Search Results - "Chakravarty, Devlina"

Identification of a covert evolutionary pathway between two protein folds by Chakravarty, Devlina, Sreenivasan, Shwetha, Swint-Kruse, Liskin, Porter, Lauren L.

“…Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and β-sheets. Such…”
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AlphaFold predictions of fold-switched conformations are driven by structure memorization by Chakravarty, Devlina, Schafer, Joseph W., Chen, Ethan A., Thole, Joseph F., Ronish, Leslie A., Lee, Myeongsang, Porter, Lauren L.

“…Recent work suggests that AlphaFold (AF)–a deep learning-based model that can accurately infer protein structure from sequence–may discern important features…”
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Plausible blockers of Spike RBD in SARS-CoV2—molecular design and underlying interaction dynamics from high-level structural descriptors by Basu, Sankar, Chakravarty, Devlina, Bhattacharyya, Dhananjay, Saha, Pampa, Patra, Hirak K

“…COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor,…”
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How to choose templates for modeling of protein complexes: Insights from benchmarking template‐based docking by Chakravarty, Devlina, McElfresh, GW, Kundrotas, Petras J., Vakser, Ilya A.

“…Comparative docking is based on experimentally determined structures of protein‐protein complexes (templates), following the paradigm that proteins with…”
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Flexibility in the N-terminal actin-binding domain: Clues from in silico mutations and molecular dynamics by Chakravarty, Devlina, Chakraborti, Soumyananda, Chakrabarti, Pinak

“…ABSTRACT Dystrophin is a long, rod‐shaped cytoskeleton protein implicated in muscular dystrophy (MDys). Utrophin is the closest autosomal homolog of…”
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Editorial: From the hydrophobic core to the globular-disorder interface: New challenges and insights into protein design by Basu, Sankar, Chakravarty, Devlina, Hou, Qingzhen, Uversky, Vladimir N

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Effects of Small Molecule Calcium-Activated Chloride Channel Inhibitors on Structure and Function of Accessory Cholera Enterotoxin (Ace) of Vibrio cholerae by Chatterjee, Tanaya, Sheikh, Irshad Ali, Chakravarty, Devlina, Chakrabarti, Pinak, Sarkar, Paramita, Saha, Tultul, Chakrabarti, Manoj K, Hoque, Kazi Mirajul

“…Cholera pathogenesis occurs due to synergistic pro-secretory effects of several toxins, such as cholera toxin (CTX) and Accessory cholera enterotoxin (Ace)…”
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The assessment of osteoporosis risk factors in Iranian women compared with Indian women by Keramat, Afsaneh, Patwardhan, Bhushan, Larijani, Bagher, Chopra, Arvind, Mithal, Ambrish, Chakravarty, Devlina, Adibi, Hossein, Khosravi, Ahmad

“…Osteoporosis is an important public health problem in older adults. It is more common in postmenopausal women and not only gives rise to morbidity but also…”
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Changes in protein structure at the interface accompanying complex formation by Chakravarty, Devlina, Janin, Joël, Robert, Charles H, Chakrabarti, Pinak

“…Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another…”
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Intrinsically disordered proteins/regions and insight into their biomolecular interactions by Chakrabarti, Pinak, Chakravarty, Devlina

“…Proteins may vary from being rigid to having flexible regions to being completely disordered, either as an intrinsically disordered protein (IDP) or having…”
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Comparison of Full and Interface Structure Alignment in Template-Based Protein Docking by Chakravarty, Devlina

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AlphaFold2 fails to predict protein fold switching by Chakravarty, Devlina, Porter, Lauren L.

“…AlphaFold2 has revolutionized protein structure prediction by leveraging sequence information to rapidly model protein folds with atomic‐level accuracy…”
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Structural changes in DNA-binding proteins on complexation by Poddar, Sayan, Chakravarty, Devlina, Chakrabarti, Pinak

“…Abstract Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We…”
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Distinguishing features of fold‐switching proteins by Chakravarty, Devlina, Schafer, Joseph W., Porter, Lauren L.

“…Though many folded proteins assume one stable structure that performs one function, a small‐but‐increasing number remodel their secondary and tertiary…”
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Interaction of Polyethyleneimine-Functionalized ZnO Nanoparticles with Bovine Serum Albumin by Chakraborti, Soumyananda, Joshi, Prachi, Chakravarty, Devlina, Shanker, Virendra, Ansari, Z. A, Singh, Surinder P, Chakrabarti, Pinak

“…In biological fluids, nanoparticles are always surrounded by proteins. As the protein is adsorbed on the surface, the extent of adsorption and the effect on…”
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Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies by Mukherjee, Debadrita, Pal, Aritrika, Chakravarty, Devlina, Chakrabarti, Pinak

“…HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus…”
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Identification and prediction of fold-switching proteins by Porter, Lauren L., Schafer, Joseph W., Chakravarty, Devlina, Kim, Allen, Rimal, Swechha, Looger, Loren, Majumdar, Ananya K., Starich, Mary, Strub, Marie-Paule

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Structural motifs in protein cores and at protein–protein interfaces are different by Hadarovich, Anna, Chakravarty, Devlina, Tuzikov, Alexander V., Ben‐Tal, Nir, Kundrotas, Petras J., Vakser, Ilya A.

“…Structures of proteins and protein–protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time,…”
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Determining the roles of a conserved tyrosine residue in a Mip-like peptidyl-prolyl cis–trans isomerase by Polley, Soumitra, Chakravarty, Devlina, Chakrabarti, Gopal, Sau, Subrata

“…The FKBP22 and the related peptidyl-prolyl cis–trans isomerases dimerize using their N-terminal domains. Conversely, their C-terminal domains possess both the…”
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Differential processing of quorum sensing signals through phosphotransfer: structural insights from molecular dynamics simulations by Chakravarty, Devlina, Chakrabarti, Pinak, Banerjee, Mousumi

“…The auto-inducer-mediated virulence gene expression and biofilm formation in Vibrio sp. uses a highly evolved two-component phosphotransfer system, involving a…”
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