Published in BMC Bioinformatics on January 26, 2007
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
A statistical framework to evaluate virtual screening. BMC Bioinformatics (2009) 1.14
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. Proteins (2010) 0.86
Application of consensus scoring and principal component analysis for virtual screening against β-secretase (BACE-1). PLoS One (2012) 0.84
Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes. J Comput Aided Mol Des (2014) 0.75
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng (1995) 19.22
Development and validation of a genetic algorithm for flexible docking. J Mol Biol (1997) 14.36
A geometric approach to macromolecule-ligand interactions. J Mol Biol (1982) 5.71
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des (1997) 5.71
In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis. J Cell Biol (1998) 3.38
Heat shock protein 90 as a molecular target for cancer therapeutics. Cancer Cell (2003) 3.25
A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem (1999) 2.98
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem (2000) 2.35
Detailed analysis of scoring functions for virtual screening. J Med Chem (2001) 2.18
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem (1999) 2.11
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem (2002) 2.10
Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry (2005) 1.62
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem (2005) 1.50
Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem (2005) 1.42
Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J Med Chem (2002) 1.38
Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comput Sci (2003) 1.37
Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys (2006) 1.34
Successful virtual screening of a chemical database for farnesyltransferase inhibitor leads. J Med Chem (2000) 1.11
Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. J Chem Inf Model (2006) 1.05
Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening. J Med Chem (2004) 1.05
Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem (1999) 0.99
The use of consensus scoring in ligand-based virtual screening. J Chem Inf Model (2006) 0.90
Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in scoring function design. J Mol Graph Model (2003) 0.87
Adenine derived inhibitors of the molecular chaperone HSP90-SAR explained through multiple X-ray structures. Bioorg Med Chem Lett (2004) 0.86
Virtual screening: a real screening complement to high-throughput screening. Biochem Soc Trans (2002) 0.85
Impact of scoring functions on enrichment in docking-based virtual screening: an application study on renin inhibitors. J Chem Inf Comput Sci (2004) 0.84
Crystal structures of human HSP90alpha-complexed with dihydroxyphenylpyrazoles. Bioorg Med Chem Lett (2005) 0.84
Ligand bias of scoring functions in structure-based virtual screening. J Chem Inf Model (2006) 0.84
Predicting protein-ligand binding affinities: a low scoring game? Org Biomol Chem (2004) 0.83
New approach to molecular docking and its application to virtual screening of chemical databases J Chem Inf Comput Sci (2000) 0.79
Making virtual screening a reality. Proc Natl Acad Sci U S A (2003) 0.77
Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. J Chem Inf Model (2008) 1.69
L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics (2003) 1.61
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res (2006) 1.57
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics (2010) 1.48
Understanding the functional roles of amino acid residues in enzyme catalysis. J Mol Biol (2009) 1.33
MACiE: a database of enzyme reaction mechanisms. Bioinformatics (2005) 1.32
Chemistry in bioinformatics. BMC Bioinformatics (2005) 1.18
Random forest models to predict aqueous solubility. J Chem Inf Model (2007) 1.15
In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window. J Chem Inf Model (2013) 1.12
Why are some properties more difficult to predict than others? A study of QSPR models of solubility, melting point, and Log P. J Chem Inf Model (2008) 1.06
Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification. J R Soc Interface (2012) 1.05
Using reaction mechanism to measure enzyme similarity. J Mol Biol (2007) 1.04
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol (2010) 1.00
A structure-odour relationship study using EVA descriptors and hierarchical clustering. Org Biomol Chem (2004) 0.99
The chemistry of protein catalysis. J Mol Biol (2007) 0.98
A novel hybrid ultrafast shape descriptor method for use in virtual screening. Chem Cent J (2008) 0.97
Classifying molecules using a sparse probabilistic kernel binary classifier. J Chem Inf Model (2011) 0.96
1,4-benzodiazepines as inhibitors of respiratory syncytial virus. The identification of a clinical candidate. J Med Chem (2007) 0.95
Predicting phospholipidosis using machine learning. Mol Pharm (2010) 0.94
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. J Comput Aided Mol Des (2007) 0.92
Chemoinformatics-based classification of prohibited substances employed for doping in sport. J Chem Inf Model (2006) 0.92
Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin Drug Metab Toxicol (2009) 0.91
PFClust: a novel parameter free clustering algorithm. BMC Bioinformatics (2013) 0.90
From sequence to enzyme mechanism using multi-label machine learning. BMC Bioinformatics (2014) 0.90
Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": significance for the validation of scoring functions. J Chem Inf Model (2011) 0.89
Is EC class predictable from reaction mechanism? BMC Bioinformatics (2012) 0.89
Communication and re-use of chemical information in bioscience. BMC Bioinformatics (2005) 0.89
Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization. J Chem Inf Model (2006) 0.87
Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. FEBS J (2011) 0.86
Predicting intrinsic aqueous solubility by a thermodynamic cycle. Mol Pharm (2008) 0.85
The geometry of interactions between catalytic residues and their substrates. J Mol Biol (2007) 0.83
Predicting protein-ligand binding affinities: a low scoring game? Org Biomol Chem (2004) 0.83
Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases. Toxicol Appl Pharmacol (2008) 0.78
Is experimental data quality the limiting factor in predicting the aqueous solubility of druglike molecules? Mol Pharm (2014) 0.77
One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees. J Mol Evol (2014) 0.77
Can we predict lattice energy from molecular structure? Acta Crystallogr B (2003) 0.76
Predicting targets of compounds against neurological diseases using cheminformatic methodology. J Comput Aided Mol Des (2014) 0.76
Enzyme informatics. Curr Top Med Chem (2012) 0.76
How to winnow actives from inactives: introducing molecular orthogonal sparse bigrams (MOSBs) and multiclass Winnow. J Chem Inf Model (2008) 0.76
Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules. J Chem Inf Model (2014) 0.75