Strength of hydrogen bonds in helices. - Nidhi Arora; B. Jayaram 001 (J. Comput. Chem., 1997)

Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level. - B. Jayaram 001; K. McConnell; Surjit B. Dixit; A. Das; David L. Beveridge (J. Comput. Chem., 2002)

From Gene to Drug: A Proof of Concept for a Plausible Computational Pathway. - Sandhya Shenoy; Bhyravabhotla Jayaram; N. Latha; Pooja Narang; Tarun Jain; Kumkum Bhushan; Saher Afshan Shaikh; Surojit Bose; Pankaj Sharma 002; Poonam Singhal; A. Gandhimathi; Praveen Agrawal; et al. (ISDA (1), 2006)

A Physicochemical Model for Analyzing DNA Sequences. - Samrat Dutta; Poonam Singhal; Praveen Agrawal; Raju Tomer; Kritee; Ekta Khurana; Bhyravabhotla Jayaram (J. Chem. Inf. Model., 2006)

Sequence and structural features of binding site residues in protein-protein complexes. - M. Michael Gromiha; N. Saranya; Samuel Selvaraj; B. Jayaram 001; Kazuhiko Fukui (BIBM, 2010)

Bhageerath: A Web Enabled High Performance Computing (HPC) Software Suite for Predicting The Tertiary Structures of Small Globular Proteins Using all Atom Energy Based Ab initio Methods. - Shashank Shekhar; Priyanka Dhingra; Bharat Lakhani; Avinash Mishra; Bhyravabhotla Jayaram (BIOCOMP, 2010)

Identification and Analysis of Binding Site Residues in Protein Complexes: Energy Based Approach. - M. Michael Gromiha; Samuel Selvaraj; B. Jayaram 001; Kazuhiko Fukui (ICIC (1), 2010)

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets. - Goutam Mukherjee; Niladri Patra; Poranjyoti Barua; Bhyravabhotla Jayaram (J. Comput. Chem., 2011)

AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors. - Tanya Singh; D. Biswas; Bhyravabhotla Jayaram (J. Chem. Inf. Model., 2011)

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. - Bhyravabhotla Jayaram; Tanya Singh; Goutam Mukherjee; Abhinav Mathur; Shashank Shekhar; Vandana Shekhar (BMC Bioinform., 2012)

ANGDelMut - a web-based tool for predicting and analyzing functional loss mechanisms of deleterious angiogenin mutations causing amyotrophic lateral sclerosis. - Aditya K. Padhi; Suhas V. Vasaikar; Bhyravabhotla Jayaram; James Gomes (F1000Research, 2013)

A homology/ab initio hybrid algorithm for sampling near-native protein conformations. - Priyanka Dhingra; Bhyravabhotla Jayaram (J. Comput. Chem., 2013)

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. - Bhyravabhotla Jayaram; Priyanka Dhingra; Avinash Mishra; Rahul Kaushik; Goutam Mukherjee; Ankita Singh; Shashank Shekhar (BMC Bioinform., 2014)

Rapid computation and interpretation of Boolean attractors in biological networks. - Suhas V. Vasaikar; Bhyravabhotla Jayaram; James Gomes (J. Complex Networks, 2015)

Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes. - Navneet Tomar; Akhilesh Mishra; Nirotpal Mrinal; B. Jayaram 001 (Database J. Biol. Databases Curation, 2016)

A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics. - Anjali Soni; Pooja Khurana; Tanya Singh; Bhyravabhotla Jayaram (Bioinform., 2017)

A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level. - Debarati DasGupta; Varun Mandalaparthy; Bhyravabhotla Jayaram (J. Comput. Chem., 2017)

PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome. - Ankita Singh; Rahul Kaushik; Himani Kuntal; B. Jayaram 001 (Database J. Biol. Databases Curation, 2018)

Systematic analysis of genes and diseases using PheWAS-Associated networks. - Ali Khosravi; Morteza Kouhsar; Bahram Goliaei; B. Jayaram 001; Ali Masoudi-Nejad (Comput. Biol. Medicine, 2019)

Ab initio Protein Structure Prediction. - Rahul Kaushik; Ankita Singh; B. Jayaram 001 (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

PvP01-DB: computational structural and functional characterization of soluble proteome of PvP01 strain of Plasmodium vivax. - Ankita Singh; Rahul Kaushik; Dheeraj Kumar Chaurasia; Manpreet Singh; B. Jayaram 001 (Database J. Biol. Databases Curation, 2020)

A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics. - Akhilesh Mishra; Sahil Dhanda; Priyanka Siwach; Shruti Aggarwal; B. Jayaram 001 (Bioinform., 2020)

Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method. - Anjali Soni; Ruchika Bhat; Bhyravabhotla Jayaram (J. Comput. Aided Mol. Des., 2020)