A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting...
BACKGROUND: Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches for protein secondary structu...
BACKGROUND: Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding protein tertiary...
Percolator is an important tool for greatly improving the results of a database search and subsequent downstream analysis. Using support vector machines (SVMs), Percolator recalibrates peptide-spectrum matches based on the learned decision boundary b...
International journal of molecular sciences
Mar 29, 2018
Protein-protein interactions (PPI) are key to protein functions and regulations within the cell cycle, DNA replication, and cellular signaling. Therefore, detecting whether a pair of proteins interact is of great importance for the study of molecular...
International journal of molecular sciences
Mar 28, 2018
Several methods have been developed to predict effects of amino acid substitutions on protein stability. Benchmark datasets are essential for method training and testing and have numerous requirements including that the data is representative for the...
Designing protein sequences that can fold into a given structure is a well-known inverse protein-folding problem. One important characteristic to attain for a protein design program is the ability to recover wild-type sequences given their native bac...
The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of th...
The receptor-associated protein (RAP) is an inhibitor of endocytic receptors that belong to the lipoprotein receptor gene family. In this study, a computational approach was tried to find the evolutionarily related fold of the RAP proteins. Through t...
Journal of chemical information and modeling
Feb 22, 2018
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geomet...