Published in J Comput Aided Mol Des on February 01, 2002
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol (2007) 2.13
Evaluating docking methods for prediction of binding affinities of small molecules to the G protein betagamma subunits. J Chem Inf Model (2009) 0.85
Drug design for ever, from hype to hope. J Comput Aided Mol Des (2012) 0.85
Improving performance of docking-based virtual screening by structural filtration. J Mol Model (2009) 0.83
An integrated approach to knowledge-driven structure-based virtual screening. J Comput Aided Mol Des (2014) 0.82
Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand. PLoS One (2015) 0.82
Combining docking with pharmacophore filtering for improved virtual screening. J Cheminform (2009) 0.81
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. J Comput Aided Mol Des (2007) 0.81
In Silico screening on the three-dimensional model of the Plasmodium vivax SUB1 protease leads to the validation of a novel anti-parasite compound. J Biol Chem (2013) 0.81
IKKβ inhibitor identification: a multi-filter driven novel scaffold. BMC Bioinformatics (2010) 0.80
Molecular modelling studies on the ORL1-receptor and ORL1-agonists. J Comput Aided Mol Des (2003) 0.79
ProPose: a docking engine based on a fully configurable protein-ligand interaction model. J Mol Model (2004) 0.78
Ultrafast de novo docking combining pharmacophores and combinatorics. J Comput Aided Mol Des (2007) 0.77
Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des (2009) 0.77
Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. PLoS One (2015) 0.75
Synthesis, urease inhibition, antioxidant, antibacterial, and molecular docking studies of 1,3,4-oxadiazole derivatives. ISRN Pharmacol (2012) 0.75
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. J Comput Aided Mol Des (2016) 0.75
Docking-undocking combination applied to the D3R Grand Challenge 2015. J Comput Aided Mol Des (2016) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
A fast flexible docking method using an incremental construction algorithm. J Mol Biol (1996) 7.33
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem (1985) 6.09
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des (1994) 3.12
Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol (2000) 2.86
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins (1999) 2.30
FlexE: efficient molecular docking considering protein structure variations. J Mol Biol (2001) 2.05
High-throughput docking for lead generation. Curr Opin Chem Biol (2001) 1.74
The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des (1992) 1.66
SuperStar: a knowledge-based approach for identifying interaction sites in proteins. J Mol Biol (1999) 1.63
A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists. J Comput Aided Mol Des (1993) 1.35
Feature trees: a new molecular similarity measure based on tree matching. J Comput Aided Mol Des (1998) 1.30
X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins. J Mol Biol (1996) 1.08
Subnanomolar Inhibitors from Computer Screening: A Model Study Using Human Carbonic Anhydrase II. Angew Chem Int Ed Engl (2001) 1.04
Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des (1997) 1.02
Recent advances in structure-based rational drug design. Curr Opin Struct Biol (2000) 0.99
Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des (1996) 0.94
Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method. J Chem Inf Comput Sci (1998) 0.90
Similarity-driven flexible ligand docking. Proteins (2000) 0.87
Structure-based virtual screening protocols. Curr Opin Drug Discov Devel (2001) 0.84
PRO_LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides. J Comput Aided Mol Des (1995) 0.76
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinformatics (2006) 1.33
Combining global and local measures for structure-based druggability predictions. J Chem Inf Model (2012) 1.27
From structure diagrams to visual chemical patterns. J Chem Inf Model (2010) 1.16
Novel technologies for virtual screening. Drug Discov Today (2004) 1.13
Modeling of metal interaction geometries for protein-ligand docking. Proteins (2008) 1.12
Beyond the virtual screening paradigm: structure-based searching for new lead compounds. J Chem Inf Model (2009) 1.10
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics (2012) 1.06
Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discov Today (2013) 1.04
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. J Comput Aided Mol Des (2011) 1.04
Recore: a fast and versatile method for scaffold hopping based on small molecule crystal structure conformations. J Chem Inf Model (2007) 1.03
From modeling to medicinal chemistry: automatic generation of two-dimensional complex diagrams. ChemMedChem (2007) 1.01
Analyzing the topology of active sites: on the prediction of pockets and subpockets. J Chem Inf Model (2010) 1.00
Towards an integrated description of hydrogen bonding and dehydration: decreasing false positives in virtual screening with the HYDE scoring function. ChemMedChem (2008) 0.96
NAOMI: on the almost trivial task of reading molecules from different file formats. J Chem Inf Model (2011) 0.93
On the art of compiling and using 'drug-like' chemical fragment spaces. ChemMedChem (2008) 0.92
FlexNovo: structure-based searching in large fragment spaces. ChemMedChem (2006) 0.88
From activity cliffs to target-specific scoring models and pharmacophore hypotheses. ChemMedChem (2011) 0.87
Multiple-ligand-based virtual screening: methods and applications of the MTree approach. J Med Chem (2005) 0.87
FlexX-Scan: fast, structure-based virtual screening. Proteins (2004) 0.85
Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J Cheminform (2009) 0.85
Automated drawing of structural molecular formulas under constraints. J Chem Inf Comput Sci (2004) 0.84
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. J Comput Aided Mol Des (2012) 0.84
CONFECT: conformations from an expert collection of torsion patterns. ChemMedChem (2013) 0.84
Predicting enzymatic function from global binding site descriptors. Proteins (2012) 0.83
Reading PDB: perception of molecules from 3D atomic coordinates. J Chem Inf Model (2012) 0.83
Novel β-amino acid derivatives as inhibitors of cathepsin A. J Med Chem (2012) 0.83
Fast protein binding site comparison via an index-based screening technology. J Chem Inf Model (2013) 0.82
Facing the challenges of structure-based target prediction by inverse virtual screening. J Chem Inf Model (2014) 0.82
Unique ring families: a chemically meaningful description of molecular ring topologies. J Chem Inf Model (2012) 0.82
An integrated approach to knowledge-driven structure-based virtual screening. J Comput Aided Mol Des (2014) 0.82
Design of combinatorial libraries for the exploration of virtual hits from fragment space searches with LoFT. J Chem Inf Model (2011) 0.82
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. J Comput Aided Mol Des (2007) 0.81
MONA - Interactive manipulation of molecule collections. J Cheminform (2013) 0.81
Torsion angle preferences in druglike chemical space: a comprehensive guide. J Med Chem (2013) 0.80
Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies. J Chem Inf Model (2006) 0.80
Fast force field-based optimization of protein-ligand complexes with graphics processor. J Comput Chem (2012) 0.79
Protein pocket and ligand shape comparison and its application in virtual screening. J Comput Aided Mol Des (2013) 0.79
Inhibition of CatA: an emerging strategy for the treatment of heart failure. Future Med Chem (2013) 0.79
SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering. J Chem Inf Model (2007) 0.78
Feasibility of Active Machine Learning for Multiclass Compound Classification. J Chem Inf Model (2016) 0.78
In silico design, synthesis, and screening of novel deoxyhypusine synthase inhibitors targeting HIV-1 replication. ChemMedChem (2014) 0.78
TFD: Torsion Fingerprints as a new measure to compare small molecule conformations. J Chem Inf Model (2012) 0.77
The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space. Mol Inform (2012) 0.77
The valence state combination model: a generic framework for handling tautomers and protonation states. J Chem Inf Model (2014) 0.77
Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des (2009) 0.77
Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. J Cheminform (2012) 0.77
Benchmark data sets for structure-based computational target prediction. J Chem Inf Model (2014) 0.76
LoFT: similarity-driven multiobjective focused library design. J Chem Inf Model (2010) 0.76
Interactive design of generic chemical patterns. Drug Discov Today (2013) 0.76
De novo design by pharmacophore-based searches in fragment spaces. J Comput Aided Mol Des (2011) 0.76
Exploiting structural information for drug-target assessment. Future Med Chem (2014) 0.76
Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias. Invest New Drugs (2012) 0.76
Searching for recursively defined generic chemical patterns in nonenumerated fragment spaces. J Chem Inf Model (2013) 0.76
Computational biotechnology: prediction of competitive substrate inhibition of enzymes by buffer compounds with protein-ligand docking. J Biotechnol (2012) 0.75
Exploring fragment spaces under multiple physicochemical constraints. J Comput Aided Mol Des (2007) 0.75
Letter from the editors. J Chem Inf Model (2015) 0.75
Improving similarity-driven library design: customized matching and regioselective feature trees. J Chem Inf Model (2011) 0.75
Searching for substructures in fragment spaces. J Chem Inf Model (2012) 0.75
What is the potential of structure-based target prediction methods? Future Med Chem (2014) 0.75
Consistent two-dimensional visualization of protein-ligand complex series. J Cheminform (2011) 0.75
Corrigendum: The Art of Compiling Protein Binding Site Ensembles. Mol Inform (2017) 0.75
Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. J Chem Inf Model (2009) 0.75
10th ICCS/GCC Conference: 40 Years of Cheminformatics. J Chem Inf Model (2015) 0.75