Carbohydrate–protein interactions: Molecular modeling insights
S Perez, I Tvaroška - Advances in carbohydrate chemistry and biochemistry, 2014 - Elsevier
The article reviews the significant contributions to, and the present status of, applications of
computational methods for the characterization and prediction of protein–carbohydrate …
computational methods for the characterization and prediction of protein–carbohydrate …
Docking validation resources: protein family and ligand flexibility experiments
A database consisting of 780 ligand− receptor complexes, termed SB2010, has been
derived from the Protein Databank to evaluate the accuracy of docking protocols for …
derived from the Protein Databank to evaluate the accuracy of docking protocols for …
Evaluation of DOCK 6 as a pose generation and database enrichment tool
In conjunction with the recent American Chemical Society symposium titled “Docking and
Scoring: A Review of Docking Programs” the performance of the DOCK6 program was …
Scoring: A Review of Docking Programs” the performance of the DOCK6 program was …
Characterizing loop dynamics and ligand recognition in human-and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free …
The comparative dynamics and inhibitor binding free energies of group-1 and group-2
pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological …
pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological …
Zwitterionic structures: from physicochemical properties toward computer-aided drug designs
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct
physicochemical properties relative to ordinary ampholytes, which largely decide their …
physicochemical properties relative to ordinary ampholytes, which largely decide their …
Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435
Hepatitis C virus (HCV) NS3/4A protease represents an attractive drug target for antiviral
therapy. However, drug resistance often occurs, making many protease inhibitors ineffective …
therapy. However, drug resistance often occurs, making many protease inhibitors ineffective …
Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons
TE Balius, S Mukherjee… - Journal of computational …, 2011 - Wiley Online Library
A docking-rescoring method, based on per-residue van der Waals (VDW), electrostatic (ES),
or hydrogen bond (HB) energies has been developed to aid discovery of ligands that have …
or hydrogen bond (HB) energies has been developed to aid discovery of ligands that have …
Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: determinants of H5N1 avian influenza virus neuraminidase …
Free-energy changes are essential physicochemical quantities for understanding most
biochemical processes. Yet, the application of accurate thermodynamic-integration (TI) …
biochemical processes. Yet, the application of accurate thermodynamic-integration (TI) …
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective
Hemagglutinin (HA) binds to sialylated glycans exposed on the host cell surface in the initial
stage of avian influenza virus infection. It has been previously hypothesized that glycan …
stage of avian influenza virus infection. It has been previously hypothesized that glycan …
Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach
Since March 2009, the rapid spread of infection during the recent A/H1N1 swine flu
pandemic has raised concerns of a far more dangerous outcome should this virus become …
pandemic has raised concerns of a far more dangerous outcome should this virus become …