1) Subramaniam, S. and Senes, A. (2012), "An energy-based conformer library for side chain optimization: Improved prediction and adjustable sampling."
Proteins: Structure, Function and Bioinformatics.
2) Kulp, D. W., Subramaniam, S., Donald, J. E., Hannigan, B. T., Mueller, B. K., Grigoryan, G. and Senes, A. (2012), "Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL).
" J. Comput. Chem.
3) LaPointe L, Taylor K, Subramaniam S; Khadria A, Rayment I, Senes A.(2012) "Structural organization of FtsB, a transmembrane protein of the bacterial divisome"
, Biochemistry 2013.
4) Subramaniam S and Senes A.(2013) "A backbone-dependant energy-based conformer library improves sidechain optimization", manuscript in preparation.
5) Subramaniam S*, Mueller BK*, Senes A. (2013) "CATM: High resolution structure prediction of trans-membrane helical dimers"
, manuscript in preparation.
1) Subramaniam S, Natarajan S, and Senes A. "A Machine Learning based Approach to Improve Protein Sidechain Optimization", Association for Computing Machinery, Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB '11) 2011 pg.478-480 [short paper] [talk]
1) Subramaniam S, Senes A. "An energy trained conformer library for sidechain optimization", From Computational Biophysics to Computational Biology (CBSB '10), June 6-8, 2010 Traverse City, Michigan [pdf]
2) Subramaniam S, Natarajan S,Senes A. "A machine learning based approach to improve sidechain optimization", Association for Computing Machinery, Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB '11), August 1-3,2011 Chicago, Illinois [pdf]
1) CIBM Seminar(BMI 915) September 20, 2011. "Efficient Conformer Libraries to improve sidechain optimization."[pdf]
2) IPiB Seminar March 30, 2012. "Predicting Protein Sidechain Conformations - A New Strategy."[pdf]
3) From Computational Biophysics to Systems Biology May 19, 2013. "Structure Prediction of Transmembrane Helix Association".[pdf]