Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data

Computer Aided Molecular Modeling Of Membrane Metalloprotease

Molecular modeling is a set of computational techniques for construction of 3D structure of a protein especially membrane bound proteins whose structures can not be elucidated using experimental techniques. These techniques has been applied in the study of membrane metalloproteases for comparing wild and mutated enzymes, docking inhibitors in the catalytic site and examination of binding pocket...

Computer-aided design software for cus- tom nucleic acid nanostructures

Modelsaz: An Object-Oriented Computer-Aided Modeling Environment

Modeling and simulation of processing plants are widely used in industry. Construction of a mathematical model for a plant is a time-consuming and error-prone task. In light of extensive advancements in computer science (both hardware and software), computers are becoming a necessary instrument in industrial activities. Many software tools for modeling, simulation and optimization of proces...

Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

MOTIVATION There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV and the RecA DNA repair protein in bacteria. The presence of such proteins can strongly alter the secondary structure of the nucleic acid molecules. Therefore, accurate modeling of the interaction between single-stranded nucleic acids and such proteins is essential to f...

Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications

Accurate prediction of pseudoknotted nucleic acid secondary structure is an important computational challenge. Prediction algorithms based on dynamic programming aim to find a structure with minimum free energy according to some thermodynamic ("sum of loop energies") model that is implicit in the recurrences of the algorithm. However, a clear definition of what exactly are the loops in pseudokn...