Recognizing pitfalls in virtual screening: a critical review
The aim of virtual screening (VS) is to identify bioactive compounds through computational
means, by employing knowledge about the protein target (structure-based VS) or known …
means, by employing knowledge about the protein target (structure-based VS) or known …
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—what can we learn from earlier …
Within the last few years a considerable amount of evaluative studies has been published
that investigate the performance of 3D virtual screening approaches. Thereby, in particular …
that investigate the performance of 3D virtual screening approaches. Thereby, in particular …
Conformer generation with OMEGA: learning from the data set and the analysis of failures
PCD Hawkins, A Nicholls - Journal of chemical information and …, 2012 - ACS Publications
We recently published a high quality validation set for testing conformer generators,
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
ConfGen: a conformational search method for efficient generation of bioactive conformers
We describe the methodology, parametrization, and application of a conformational search
method, called ConfGen, designed to efficiently generate bioactive conformers. We define …
method, called ConfGen, designed to efficiently generate bioactive conformers. We define …
Molecule-pharmacophore superpositioning and pattern matching in computational drug design
Three-dimensional (3D) pharmacophore modeling is a technique for describing the
interaction of a small molecule ligand with a macromolecular target. Since chemical features …
interaction of a small molecule ligand with a macromolecular target. Since chemical features …
Efficient overlay of small organic molecules using 3D pharmacophores
Aligning and overlaying two or more bio-active molecules is one of the key tasks in
computational drug discovery and bio-activity prediction. Especially chemical-functional …
computational drug discovery and bio-activity prediction. Especially chemical-functional …
Flavonoids as protein kinase inhibitors for cancer chemoprevention: direct binding and molecular modeling
DX Hou, T Kumamoto - Antioxidants & redox signaling, 2010 - liebertpub.com
Protein kinases play crucial roles in the regulation of multiple cell signaling pathways and
cellular functions. Deregulation of protein kinase function has been implicated in …
cellular functions. Deregulation of protein kinase function has been implicated in …
Virtual screening for the discovery of bioactive natural products
JM Rollinger, H Stuppner, T Langer - Natural compounds as drugs …, 2008 - Springer
In this survey the impact of the virtual screening concept is discussed in the field of drug
discovery from nature. Confronted by a steadily increasing number of secondary metabolites …
discovery from nature. Confronted by a steadily increasing number of secondary metabolites …
Auto3d: Automatic generation of the low-energy 3d structures with ANI neural network potentials
Computational programs accelerate the chemical discovery processes but often need
proper three-dimensional molecular information as part of the input. Getting optimal …
proper three-dimensional molecular information as part of the input. Getting optimal …
Pharmacophore modeling: advances, limitations, and current utility in drug discovery
X Qing, X Yin Lee, J De Raeymaeker… - Journal of Receptor …, 2014 - Taylor & Francis
Pharmacophore modeling is a successful yet very diverse subfield of computer-aided drug
design. The concept of the pharmacophore has been widely applied to the rational design of …
design. The concept of the pharmacophore has been widely applied to the rational design of …