Latest developments in molecular docking: 2010–2011 in review

E Yuriev, PA Ramsland - Journal of Molecular Recognition, 2013 - Wiley Online Library
The aim of docking is to accurately predict the structure of a ligand within the constraints of a
receptor binding site and to correctly estimate the strength of binding. We discuss, in detail …

Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology

KY Hsin, S Ghosh, H Kitano - PloS one, 2013 - journals.plos.org
Increased availability of bioinformatics resources is creating opportunities for the application
of network pharmacology to predict drug effects and toxicity resulting from multi-target …

Fragment informatics and computational fragment‐based drug design: an overview and update

C Sheng, W Zhang - Medicinal Research Reviews, 2013 - Wiley Online Library
Fragment‐based drug design (FBDD) is a promising approach for the discovery and
optimization of lead compounds. Despite its successes, FBDD also faces some internal …

Docking challenge: protein sampling and molecular docking performance

KM Elokely, RJ Doerksen - Journal of chemical information and …, 2013 - ACS Publications
Computational tools are essential in the drug design process, especially in order to take
advantage of the increasing numbers of solved X-ray and NMR protein–ligand structures …

Nitroreductase Detection and Hypoxic Tumor Cell Imaging by a Designed Sensitive and Selective Fluorescent Probe, 7-[(5-Nitrofuran-2-yl)methoxy]-3H-phenoxazin-3 …

Z Li, X Li, X Gao, Y Zhang, W Shi, H Ma - Analytical chemistry, 2013 - ACS Publications
A highly selective and sensitive fluorescence probe, 7-[(5-nitrofuran-2-yl) methoxy]-3 H-
phenoxazin-3-one (1), is developed for imaging the hypoxic status of tumor cells via the …

Development of a natural products database from the biodiversity of Brazil

M Valli, RN Dos Santos, LD Figueira… - Journal of natural …, 2013 - ACS Publications
We describe herein the design and development of an innovative tool called the NuBBE
database (NuBBEDB), a new Web-based database, which incorporates several classes of …

Encoding protein–ligand interaction patterns in fingerprints and graphs

J Desaphy, E Raimbaud, P Ducrot… - Journal of chemical …, 2013 - ACS Publications
We herewith present a novel and universal method to convert protein–ligand coordinates
into a simple fingerprint of 210 integers registering the corresponding molecular interaction …

[HTML][HTML] Flavonoid from Carica papaya inhibits NS2B-NS3 protease and prevents Dengue 2 viral assembly

P Senthilvel, P Lavanya, KM Kumar, R Swetha… - …, 2013 - ncbi.nlm.nih.gov
Dengue virus belongs to the virus family Flaviviridae. Dengue hemorrhagic disease caused
by dengue virus is a public health problem worldwide. The viral non structural 2B and 3 …

CSAR benchmark exercise 2011–2012: evaluation of results from docking and relative ranking of blinded congeneric series

KL Damm-Ganamet, RD Smith… - Journal of chemical …, 2013 - ACS Publications
The Community Structure–Activity Resource (CSAR) recently held its first blinded exercise
based on data provided by Abbott, Vertex, and colleagues at the University of Michigan, Ann …

Identification of five structurally unrelated quorum-sensing inhibitors of Pseudomonas aeruginosa from a natural-derivative database

SYY Tan, SL Chua, Y Chen, SA Rice… - Antimicrobial agents …, 2013 - Am Soc Microbiol
Bacteria communicate by means of small signal molecules in a process termed quorum
sensing (QS). QS enables bacteria to organize their activities at the population level …