Published in Curr Opin Chem Biol on August 01, 2002
ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model (2005) 16.75
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev (2008) 2.27
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins. J Biomol NMR (2007) 1.65
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem (2009) 1.54
Computational methods in drug discovery. Pharmacol Rev (2013) 1.51
Protein dynamics and the immunological evolution of molecular recognition. Proc Natl Acad Sci U S A (2004) 1.24
Designing ligands to bind proteins. Q Rev Biophys (2006) 1.19
Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model (2010) 1.17
CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model (2013) 1.17
Probing a protein-protein interaction by in vitro evolution. Proc Natl Acad Sci U S A (2006) 1.15
Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. Biochemistry (2011) 1.14
Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10
Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. Biochemistry (2011) 1.06
In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. Proteins (2008) 1.01
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J Comput Aided Mol Des (2012) 0.99
In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking. Proteins (2009) 0.98
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput (2009) 0.98
Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures. J Chem Inf Model (2009) 0.96
Exploring the role of receptor flexibility in structure-based drug discovery. Biophys Chem (2013) 0.93
Modulation of catalytic function by differential plasticity of the active site: case study of Trypanosoma cruzi trans-sialidase and Trypanosoma rangeli sialidase. Biochemistry (2009) 0.93
Predictive power of molecular dynamics receptor structures in virtual screening. J Chem Inf Model (2011) 0.93
Computer-aided drug-discovery techniques that account for receptor flexibility. Curr Opin Pharmacol (2010) 0.92
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. J Cheminform (2013) 0.89
Novel method for probing the specificity binding profile of ligands: applications to HIV protease. Chem Biol Drug Des (2008) 0.87
Design of growth factor sequestering biomaterials. Chem Commun (Camb) (2014) 0.87
Significant enhancement of docking sensitivity using implicit ligand sampling. J Chem Inf Model (2011) 0.86
Molecular recognition in the case of flexible targets. Curr Pharm Des (2011) 0.85
Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery. BMC Struct Biol (2010) 0.85
Docking and scoring of metallo-beta-lactamases inhibitors. J Comput Aided Mol Des (2004) 0.85
Utilizing experimental data for reducing ensemble size in flexible-protein docking. J Chem Inf Model (2011) 0.84
Virtual high throughput screening (vHTS)--a perspective. Bioinformation (2008) 0.83
An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. J Med Chem (2014) 0.82
Identification of xenoestrogens in food additives by an integrated in silico and in vitro approach. Chem Res Toxicol (2009) 0.82
The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease. ACS Chem Neurosci (2012) 0.82
Three-dimensional compound comparison methods and their application in drug discovery. Molecules (2015) 0.81
Protein conformational flexibility prediction using machine learning. J Magn Reson (2008) 0.81
Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Sci (2010) 0.81
A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform (2016) 0.79
Investigating the dynamic aspects of drug-protein recognition through a combination of MD and NMR analyses: implications for the development of protein-protein interaction inhibitors. PLoS One (2014) 0.79
Comparing neural-network scoring functions and the state of the art: applications to common library screening. J Chem Inf Model (2013) 0.79
Computational molecular modeling for evaluating the toxicity of environmental chemicals: prioritizing bioassay requirements. Environ Health Perspect (2008) 0.79
MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol Biol (2013) 0.78
Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. Eur Biophys J (2010) 0.78
Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein. J Comput Aided Mol Des (2008) 0.78
Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking. J Chem Phys (2012) 0.78
BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states. BMC Res Notes (2011) 0.77
From protein structure to function via single crystal optical spectroscopy. Front Mol Biosci (2015) 0.77
Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. J Comput Chem (2015) 0.76
A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity. Biophys J (2006) 0.76
Approximating protein flexibility through dynamic pharmacophore models: application to fatty acid amide hydrolase (FAAH). J Chem Inf Model (2011) 0.76
Discovery of Novel ROCK1 Inhibitors via Integrated Virtual Screening Strategy and Bioassays. Sci Rep (2015) 0.76
A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid. Biophys J (2007) 0.76
Conformational transition paths harbor structures useful for aiding drug discovery and understanding enzymatic mechanisms in protein kinases. Protein Sci (2015) 0.75
Effect of Biomolecular Conformation on Docking Simulation: A Case Study on a Potent HIV-1 Protease Inhibitor. Iran J Pharm Res (2015) 0.75
Stabilization of anionic and neutral forms of a fluorophoric ligand at the active site of human carbonic anhydrase I. Biochim Biophys Acta (2010) 0.75
Structure of ring-shaped Aβ42 oligomers determined by conformational selection. Sci Rep (2016) 0.75
PeptiSite: a structural database of peptide binding sites in 4D. Biochem Biophys Res Commun (2014) 0.75
Druggability analysis and classification of protein tyrosine phosphatase active sites. Drug Des Devel Ther (2016) 0.75
Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC. J Comput Aided Mol Des (2013) 0.75
Low potency toxins reveal dense interaction networks in metabolism. BMC Syst Biol (2016) 0.75
Induced fit docking, and the use of QM/MM methods in docking. Drug Discov Today Technol (2013) 0.75
Molecular dynamics simulations of hsp90 with an eye to inhibitor design. Pharmaceuticals (Basel) (2012) 0.75
Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential. PLoS One (2017) 0.75
Development and testing of a de novo drug-design algorithm. J Comput Aided Mol Des (2003) 0.75