Computational Biophysics and Bioinformatics
Professor Emil Alexov Group
Congratulations to Shamrat Paul on his Master's graduation!
Dr. Alexov was awarded University Research, Scholarship and Artistic Achievement Award (URSAAA)
Dr. Shailesh K. Panday was promoted to Senior Research Scientist
Dr. Alexov was elected to the American Institute for Medical and Biological Engineering (AIMBE)
The lab was awarded R35GM151964 (MIRA) 2024-2029 of $1.9M.
Congratulations to Mahesh and Mihiri for graduating in 2022
Clemson University offers MS/PhD in Medical Biophysics. News.
Dr. Emil Alexov was named Wallace R. Roy Distinguished Professor. News.
About the Lab
The research in the lab focuses on computational modeling of biological macromolecules and their assemblages as well as predicting biophysical quantities associated with them. One of the primary roles of the lab is to develop and maintain the popular software package DelPhi, which calculates electrostatic potentials and energies of systems comprised of biological macromolecules. We are also interested in modeling disease-causing missense mutations, pKa's of amino acids and nucleic groups, and pH-dependence of stability and binding. Visit Predicagen LLC for details about services for human genetic differences and their interpretation.
Software & Servers
See repositories at 
Delphi webserver is an online interface for the popular Poisson-Boltzmann solver (Delphi) for calculating electrostatic energies and potential in biological macromolecules.
Delphi-PKA is a DelPhi-based C++ program which allows to predict pKa's for ionizable groups at given pH in proteins, RNA and DNA.
DelphiForce is a DelPhi-based script allowing to calculate electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.
A group of structure and sequece based methods for predicting protein-protein Binding Energy change due to Single Amino Acid Mutation (SAAMBE).
An online application for calculating folding free energy changes in proteins caused by missense mutations for provided protein sequence.
BION-2 predicts the positions of non-specifically surface-bound ions utilizing the Gaussian-based treatment of ions within the framework of the modified Poisson–Boltzmann equation.
PKAD - 2 contains experimentally measured pKa values for >1500 ionizable residues in wild type as well as mutant proteins.
SAMPDI-3Dv2 uses a machine learning algorithm with features as physico-chemical properties, structure of mutation site and protein-DNA interactions to predict the change of binding free energy.
Predicting protein-protein binding free energy change due to single amino acid change in membrane proteins.
The PKAD-R database is carefully curated, redesigned and expanded (including 214 new (128 non-redundant) pKa entries from the literature) upon PKAD and PKAD-2.
People
Head of Lab
Professor Emil Alexov, PhD
ealexov@g.clemson.edu
Postdoctoral Associate
Shailesh K Panday, PhD
spanday@clemson.edu
Ph.D. Student
Prawin Rimal
primal@g.clemson.edu
Ph.D. Student
Pitambar Poudel
pitambp@g.clemson.edu
Graduate Student: Medical Biophysics
Shamrat Paul
shamrap@g.clemson.edu
Graduate Student: Medical Biophysics
Ashley Wigfall
ashley.wigfall10@gmail.com
Graduate Student: Medical Biophysics
Davis Balentine Jr.
bdbalen@clemson.edu
Graduate Student: Medical Biophysics
Nirav Modha
nmodha@clemson.edu
News