Search Results - "JAYARAM, B"

C5′ omitted DNA enhances bendability and protein binding by Pant, Pradeep, Jayaram, B.

“…Protein-DNA interactions are of great biological importance. The specificity and strength of these intimate contacts are crucial in the proper functioning of a…”
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Seq2Enz: An application of mask BLAST methodology with a new chemical logic of amino acids for improved enzyme function prediction by Pathak, Amita, Jayaram, B.

“…Seq2Enz method is a new way to identify whether a query protein sequence is an enzyme and to assign an enzyme class to the protein sequence. The method is…”
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Symmetric Nucleosides as Potent Purine Nucleoside Phosphorylase Inhibitors by Pant, Pradeep, Pathak, Amita, Jayaram, B

“…Nucleic acids are one of the most enigmatic biomolecules crucial to several biological processes. Nucleic acid–protein interactions are vital for the…”
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A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics by Soni, Anjali, Khurana, Pooja, Singh, Tanya, Jayaram, B

“…Drug intercalation is an important strategy for DNA inhibition which is often employed in cancer chemotherapy. Despite its high significance, the field is…”
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Sanjeevini: a freely accessible web-server for target directed lead molecule discovery by Jayaram, B, Singh, Tanya, Mukherjee, Goutam, Mathur, Abhinav, Shekhar, Shashank, Shekhar, Vandana

“…Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target…”
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Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations by Pant, Pradeep, Pathak, Amita, Jayaram, B.

“…DNA-protein interactions occur at all levels of DNA expression and replication and are crucial determinants for the survival of a cell. Several modified…”
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AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors by Singh, Tanya, Biswas, D, Jayaram, B

“…We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder…”
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A plausible mechanism for the antimalarial activity of artemisinin: A computational approach by Shandilya, Ashutosh, Chacko, Sajeev, Jayaram, B., Ghosh, Indira

“…Artemisinin constitutes the frontline treatment to aid rapid clearance of parasitaemia and quick resolution of malarial symptoms. However, the widespread…”
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A rapid identification of hit molecules for target proteins via physico-chemical descriptors by Mukherjee, Goutam, Jayaram, B

“…We report here a novel computationally fast protocol (RASPD) for identifying good candidates for any target protein from any molecule/million molecule…”
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Molecular dynamics simulation-based trinucleotide and tetranucleotide level structural and energy characterization of the functional units of genomic DNA by Sharma, Dinesh, Sharma, Kopal, Mishra, Akhilesh, Siwach, Priyanka, Mittal, Aditya, Jayaram, B

“…Genomes of most organisms on earth are written in a universal language of life, made up of four units - adenine (A), thymine (T), guanine (G), and cytosine…”
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Rational design, synthesis and biological screening of triazine-triazolopyrimidine hybrids as multitarget anti-Alzheimer agents by Jameel, Ehtesham, Meena, Poonam, Maqbool, Mudasir, Kumar, Jitendra, Ahmed, Waqar, Mumtazuddin, Syed, Tiwari, Manisha, Hoda, Nasimul, Jayaram, B.

“…In our endeavor towards the development of potent multitarget ligands for the treatment of Alzheimer's disease, a series of triazine-triazolopyrimidine hybrids…”
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Where Informatics Lags Chemistry Leads by Kaushik, Rahul, Singh, Ankita, Jayaram, B

“…The fact that amino acid sequences dictate the tertiary structures of proteins has been known for more than five decades. While the molecular pathways to…”
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ProTSAV: A protein tertiary structure analysis and validation server by Singh, Ankita, Kaushik, Rahul, Mishra, Avinash, Shanker, Asheesh, Jayaram, B.

“…Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality…”
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A small molecule targeting hepatitis B surface antigen inhibits clinically relevant drug-resistant hepatitis B virus by Kiruthika, S, Bhat, Ruchika, Jayaram, B, Vivekanandan, Perumal

“…Abstract Background Currently approved oral antivirals for chronic HBV infection target the reverse transcriptase (RT) domain of the HBV polymerase. Emergence…”
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From Ramachandran Maps to Tertiary Structures of Proteins by DasGupta, Debarati, Kaushik, Rahul, Jayaram, B

“…Sequence to structure of proteins is an unsolved problem. A possible coarse grained resolution to this entails specification of all the torsional (Φ, Ψ) angles…”
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Symmetrization of the backbone of nucleic acids: a molecular dynamics study by Pant, Pradeep, Pathak, Amita, Jayaram, B.

“…DNA displays directional asymmetry (5'→3'), a fundamental property associated with each strand of the nucleic acids and is crucial to several biological…”
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A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics by Mishra, Akhilesh, Dhanda, Sahil, Siwach, Priyanka, Aggarwal, Shruti, Jayaram, B

“…Abstract Motivation Despite conservation in general architecture of promoters and protein–DNA interaction interface of RNA polymerases among various…”
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Structural difficulty index: a reliable measure for modelability of protein tertiary structures by Kaushik, Rahul, Jayaram, B.

“…Abstract The success in protein tertiary-structure prediction is considered to be a function of coverage and similarity/identity of their sequences with…”
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Role of solvent accessibility for aggregation-prone patches in protein folding by Mishra, Avinash, Ranganathan, Shoba, Jayaram, B., Sattar, Abdul

“…The arrangement of amino acids in a protein sequence encodes its native folding. However, the same arrangement in aggregation-prone regions may cause…”
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Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation by Rani, Anjeeta, Jayaraj, Abhilash, Jayaram, B., Pannuru, Venkatesu

“…In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress…”
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