Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC

Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

(2012) William Sinko et al.   Chemical Biology & Drug Design

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Protonation, Tautomerization, and Rotameric Structure of Histidine: A Comprehensive Study by Magic-Angle-Spinning Solid-State NMR

(2011) Shenhui Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

(2011) Sarah L. Williams et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

(2010) Ian R. Craig et al.   Journal of Chemical Information and Modeling

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

(2010) Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

(2010) Jianxin Duan et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Estimating binding affinities by docking/scoring methods using variable protonation states

(2010) Min-Sun Park et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identification of triazinoindol-benzimidazolones as nanomolar inhibitors of the Mycobacterium tuberculosis enzyme TDP-6-deoxy-d-xylo-4-hexopyranosid-4-ulose 3,5-epimerase (RmlC)

(2009) Sharmila Sivendran et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

(2009) Tim ten Brink et al.   Journal of Chemical Information and Modeling

The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening

(2009) Tuomo Kalliokoski et al.   Journal of Chemical Information and Modeling

Let’s not forget tautomers

(2009) Yvonne Connolly Martin   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

What do we know and when do we know it?

(2008) Anthony Nicholls   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS