Aromaticity from the viewpoint of molecular geometry: application to planar systems
Following the history of organic chemistry, studies on relations between chemical (and later
physicochemical) properties and the structure of chemical species in question are the heart …
physicochemical) properties and the structure of chemical species in question are the heart …
Binding of small-molecule ligands to proteins:“what you see” is not always “what you get”
We review insights from computational studies of affinities of ligands binding to proteins. The
power of structural biology is in translating knowledge of protein structures into insights …
power of structural biology is in translating knowledge of protein structures into insights …
Automated exploration of the low-energy chemical space with fast quantum chemical methods
We propose and discuss an efficient scheme for the in silico sampling for parts of the
molecular chemical space by semiempirical tight-binding methods combined with a meta …
molecular chemical space by semiempirical tight-binding methods combined with a meta …
ZINC− a free database of commercially available compounds for virtual screening
A critical barrier to entry into structure-based virtual screening is the lack of a suitable, easy
to access database of purchasable compounds. We have therefore prepared a library of 727 …
to access database of purchasable compounds. We have therefore prepared a library of 727 …
Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
JR Greenwood, D Calkins, AP Sullivan… - Journal of computer …, 2010 - Springer
Generating the appropriate protonation states of drug-like molecules in solution is important
for success in both ligand-and structure-based virtual screening. Screening collections of …
for success in both ligand-and structure-based virtual screening. Screening collections of …
Epik: pKa and Protonation State Prediction through Machine Learning
Epik version 7 is a software program that uses machine learning for predicting the p K a
values and protonation state distribution of complex, druglike molecules. Using an ensemble …
values and protonation state distribution of complex, druglike molecules. Using an ensemble …
Tautomerism unveils a self-inhibition mechanism of crystallization
Modifiers are commonly used in natural, biological, and synthetic crystallization to tailor the
growth of diverse materials. Here, we identify tautomers as a new class of modifiers where …
growth of diverse materials. Here, we identify tautomers as a new class of modifiers where …
Computations of standard binding free energies with molecular dynamics simulations
Y Deng, B Roux - The Journal of Physical Chemistry B, 2009 - ACS Publications
An increasing number of studies have reported computations of the standard (absolute)
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …
The pKa Distribution of Drugs: Application to Drug Discovery
DT Manallack - Perspectives in medicinal chemistry, 2007 - journals.sagepub.com
The acid-base dissociation constant (p K a) of a drug is a key physicochemical parameter
influencing many biopharmaceutical characteristics. While this has been well established …
influencing many biopharmaceutical characteristics. While this has been well established …
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 …