Computational Biophysics and Bioinformatics

Congratulations to Mahesh and Mihiri for graduating in 2022

The lab is continuously supported by NIH since 2010. Current grant period covers 2022 until 2026.

Clemson University offers MS/PhD in Medical Biophysics. News.

Dr. Emil Alexov was named Wallace R. Roy Distinguished Professor. News.

Strong Presence of the Biophysical Group at ACS Annual Meeting, San Diego 2021. See Abstracts.

Dr. Emil Alexov is Editor-in-Chief of the Journal of Computational Biophysics and Chemistry.

Argo Chakravorty and Angela Wu received their PhD diplomas in August 2019

Argo Chakravorty (in the middle) received the Outstanding Graduate Research Assistant award

Atomic-style Clemson Robot

Robot holding barnase-barstar complex.

Created by Brandon Campbell, ProNOI package developed by Nick Smith. Potential distribution calculated with parallelized DelPhi developed by Chuan Li. Movie created by Lin Li.

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

Delphi webserver is an online interface for the popular Poisson-Boltzmann solver (Delphi) for calculating electrostatic energies and potential in biological macromolecules.

Delphi pKa

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

DelphiForce is a DelPhi-based script allowing to calculate electrostatic force between two objects, such as proteins, DNAs, lipids, small molecules, etc.

SAMPDI

SAMPDI Web Server provides fast and accurate predictions for the effects of single amino acid substitution on the binding free energy of protein-DNA complex.

SAAMBE

A group of structure and sequece based methods for predicting protein-protein Binding Energy change due to Single Amino Acid Mutation (SAAMBE).

SAAFEC-SEQ

An online application for calculating folding free energy changes in proteins caused by missense mutations for provided protein sequence.

BION-2

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

PKAD - 2 contains experimentally measured pKa values for >1500 ionizable residues in wild type as well as mutant proteins.

SAMPDI-3D

SAMPDI-3D 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.

People

Head of Lab