What is bioinformatics? A proposed definition and overview of the field
NM Luscombe, D Greenbaum… - Methods of information …, 2001 - thieme-connect.com
Background: The recent flood of data from genome sequences and functional genomics has
given rise to new field, bioinformatics, which combines elements of biology and computer …
given rise to new field, bioinformatics, which combines elements of biology and computer …
A review of protein-small molecule docking methods
The binding of small molecule ligands to large protein targets is central to numerous
biological processes. The accurate prediction of the binding modes between the ligand and …
biological processes. The accurate prediction of the binding modes between the ligand and …
ZDOCK: an initial‐stage protein‐docking algorithm
The development of scoring functions is of great importance to protein docking. Here we
present a new scoring function for the initial stage of unbound docking. It combines our …
present a new scoring function for the initial stage of unbound docking. It combines our …
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein–protein complexes
Hydrogen bonding is a key contributor to the specificity of intramolecular and intermolecular
interactions in biological systems. Here, we develop an orientation-dependent hydrogen …
interactions in biological systems. Here, we develop an orientation-dependent hydrogen …
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
A comprehensive docking study was performed on 27 distinct protein‐protein complexes.
For 13 test systems, docking was performed with the unbound X‐ray structures of both the …
For 13 test systems, docking was performed with the unbound X‐ray structures of both the …
Recent progress and future directions in protein-protein docking
DW Ritchie - Current protein and peptide science, 2008 - ingentaconnect.com
This article gives an overview of recent progress in protein-protein docking and it identifies
several directions for future research. Recent results from the CAPRI blind docking …
several directions for future research. Recent results from the CAPRI blind docking …
Residue frequencies and pairing preferences at protein–protein interfaces
We used a nonredundant set of 621 protein–protein interfaces of known high‐resolution
structure to derive residue composition and residue–residue contact preferences. The …
structure to derive residue composition and residue–residue contact preferences. The …
Rational design of faster associating and tighter binding protein complexes
T Selzer, S Albeck, G Schreiber - Nature structural biology, 2000 - nature.com
A protein design strategy was developed to specifically enhance the rate of association (k
on) between a pair of proteins without affecting the rate of dissociation (k off). The method is …
on) between a pair of proteins without affecting the rate of dissociation (k off). The method is …
Protein–protein interfaces: analysis of amino acid conservation in homodimers
WSJ Valdar, JM Thornton - Proteins: Structure, Function, and …, 2001 - Wiley Online Library
Evolutionary information derived from the large number of available protein sequences and
structures could powerfully guide both analysis and prediction of protein–protein interfaces …
structures could powerfully guide both analysis and prediction of protein–protein interfaces …
A novel shape complementarity scoring function for protein‐protein docking
Shape complementarity is the most basic ingredient of the scoring functions for protein‐
protein docking. Most grid‐based docking algorithms use the total number of grid points at …
protein docking. Most grid‐based docking algorithms use the total number of grid points at …