Deciphering protein–protein interactions. Part I. Experimental techniques and databases
BA Shoemaker, AR Panchenko - PLoS computational biology, 2007 - journals.plos.org
Proteins interact with each other in a highly specific manner, and protein interactions play a
key role in many cellular processes; in particular, the distortion of protein interfaces may lead …
key role in many cellular processes; in particular, the distortion of protein interfaces may lead …
[HTML][HTML] Computational prediction of protein interfaces: A review of data driven methods
Reliably pinpointing which specific amino acid residues form the interface (s) between a
protein and its binding partner (s) is critical for understanding the structural and …
protein and its binding partner (s) is critical for understanding the structural and …
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
S Saha, GPS Raghava - Nucleic acids research, 2006 - academic.oup.com
In this study a systematic attempt has been made to integrate various approaches in order to
predict allergenic proteins with high accuracy. The dataset used for testing and training …
predict allergenic proteins with high accuracy. The dataset used for testing and training …
A generic method for assignment of reliability scores applied to solvent accessibility predictions
Background Estimation of the reliability of specific real value predictions is nontrivial and the
efficacy of this is often questionable. It is important to know if you can trust a given prediction …
efficacy of this is often questionable. It is important to know if you can trust a given prediction …
Predicting functionally important residues from sequence conservation
JA Capra, M Singh - Bioinformatics, 2007 - academic.oup.com
Motivation: All residues in a protein are not equally important. Some are essential for the
proper structure and function of the protein, whereas others can be readily replaced …
proper structure and function of the protein, whereas others can be readily replaced …
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
Identifying a protein's functional sites is an important step towards characterizing its
molecular function. Numerous structure-and sequence-based methods have been …
molecular function. Numerous structure-and sequence-based methods have been …
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
Motivation: Hot spots are residues comprising only a small fraction of interfaces yet
accounting for the majority of the binding energy. These residues are critical in …
accounting for the majority of the binding energy. These residues are critical in …
PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework
Determining the catalytic residues in an enzyme is critical to our understanding the
relationship between protein sequence, structure, function, and enhancing our ability to …
relationship between protein sequence, structure, function, and enhancing our ability to …
Protein binding site prediction using an empirical scoring function
Most biological processes are mediated by interactions between proteins and their
interacting partners including proteins, nucleic acids and small molecules. This work …
interacting partners including proteins, nucleic acids and small molecules. This work …
BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
Background Understanding how biomolecules interact is a major task of systems biology. To
model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding …
model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding …