B. Jayaram

发表

ParDOCK: an all atom energy based Monte Carlo docking protocol for protein-ligand complexes.

Pankaj Sharma, A. Gupta, A. Gandhimathi, 2007, Protein and peptide letters.

Free Energy Analysis of ProteinDNA Binding: The EcoRI EndonucleaseDNA Complex

Surjit B. Dixit, David L. Beveridge, Kevin J. McConnell, 1999 .

Do water molecules mediate protein-DNA recognition?

B. Jayaram, B. Jayaram, B Jayaram, 2001, Journal of molecular biology.

An overview of protein–ligand docking and scoring algorithms

B. Jayaram, B. Jayaram, A. Soni, 2020, Protein Interactions.

Use of isotope-dilution phenomenon to advantage in the determination of kinetic constants Km and Kcat for BamHI restriction endonuclease: an empirical and iterative approach.

B. Jayaram, K. B. Roy, D. Vrushank, 1994, Analytical biochemistry.

Towards a universal structural and energetic model for prokaryotic promoters

Kelly M. Thayer, M. Bansal, W. Olson, 2018, bioRxiv.

A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders.

Saher Afshan Shaikh, S. Shaikh, B. Jayaram, 2004, Archives of biochemistry and biophysics.

DNA minor groove binding of small molecules: Experimental and computational evidence

G. S. Kumar, B. Jayaram, Md. Maidul Islam, 2010 .

A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm.

Saher Afshan Shaikh, S. Shaikh, B. Jayaram, 2007, Journal of medicinal chemistry.

Allosterically coupled multi-site binding of testosterone to human serum albumin.

G. Wagner, S. Bhasin, Ravi Jasuja, 2020, Endocrinology.

Identification of peptides within the base binding domains of the GTP- and ATP-specific binding sites of tubulin.

B. Jayaram, B. Haley, 1994, The Journal of biological chemistry.

Stimulation of heat shock protein 90 chaperone function through binding of a novobiocin analog KU-32

S. Deep, B. Blagg, B. Jayaram, 2019, The Journal of Biological Chemistry.

Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation

B. Jayaram, Anjeeta Rani, A. Jayaraj, 2016, Scientific Reports.

Calculation of the Affinity of the λ Repressor-Operator Complex Based on Free Energy Component Analysis

D. Kombo, D. Beveridge, K. McConnell, 2002 .

Strength of hydrogen bonds in α helices

Nidhi Arora, Bhyravabhotla Jayaram, B. Jayaram, 1997 .

A comprehensive automated computer-aided discovery pipeline from genomes to hit molecules

Shashank Shekhar, Ankita Singh, Bhyravabhotla Jayaram, 2020 .

Free‐energy component analysis of 40 protein–DNA complexes: A consensus view on the thermodynamics of binding at the molecular level

A. Das, B. Jayaram, Surjit B. Dixit, 2002, J. Comput. Chem..

Determination of the nucleotide binding site within Clostridium symbiosum pyruvate phosphate dikinase by photoaffinity labeling, site-directed mutagenesis, and structural analysis.

S. Thrall, O. Herzberg, D. Dunaway-Mariano, 1996, Biochemistry.

Ab initio Protein Structure Prediction

Ankita Singh, Bhyravabhotla Jayaram, Rahul Kaushik, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding.

B. Jayaram, B Jayaram, P Kalra, 2001, Journal of medicinal chemistry.

Free-energy analysis of enzyme-inhibitor binding

B. Jayaram, Parul Kalra, Achintya Das, 2001, Applied biochemistry and biotechnology.

Molecular dynamics simulation-based trinucleotide and tetranucleotide level structural and energy characterization of the functional units of genomic DNA.

B. Jayaram, Akhilesh Mishra, Kopal Sharma, 2023, Physical chemistry chemical physics : PCCP.

Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations.

Poonam Singhal, D. Beveridge, S. Dixit, 2008, Biophysical journal.