Published in Proteins on August 15, 2005
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res (2006) 10.36
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. Nucleic Acids Res (2006) 2.02
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res (2007) 1.99
Chemogenomic approaches to rational drug design. Br J Pharmacol (2007) 1.74
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J Chem Inf Model (2011) 1.61
CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. J Chem Inf Model (2011) 1.42
Docking validation resources: protein family and ligand flexibility experiments. J Chem Inf Model (2010) 1.25
Public domain databases for medicinal chemistry. J Med Chem (2012) 1.23
NNScore: a neural-network-based scoring function for the characterization of protein-ligand complexes. J Chem Inf Model (2010) 1.21
The Protein Data Bank archive as an open data resource. J Comput Aided Mol Des (2014) 1.20
Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise. J Chem Inf Model (2013) 1.16
Text mining improves prediction of protein functional sites. PLoS One (2012) 1.16
istar: a web platform for large-scale protein-ligand docking. PLoS One (2014) 1.14
BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model (2011) 1.12
NNScore 2.0: a neural-network receptor-ligand scoring function. J Chem Inf Model (2011) 1.12
Virtual screening using molecular simulations. Proteins (2011) 1.05
Bioinformatics and variability in drug response: a protein structural perspective. J R Soc Interface (2012) 1.01
Extent of structural asymmetry in homodimeric proteins: prevalence and relevance. PLoS One (2012) 1.00
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics (2011) 0.99
Molecular networks in drug discovery. Crit Rev Biomed Eng (2010) 0.98
Lessons for fragment library design: analysis of output from multiple screening campaigns. J Comput Aided Mol Des (2009) 0.98
Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med (2009) 0.98
Differences between high- and low-affinity complexes of enzymes and nonenzymes. J Med Chem (2008) 0.97
ProtChemSI: a network of protein-chemical structural interactions. Nucleic Acids Res (2011) 0.96
Surface-based protein binding pocket similarity. Proteins (2011) 0.95
Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries. J Chem Inf Model (2011) 0.91
HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J Mol Graph Model (2011) 0.90
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model. BMC Struct Biol (2009) 0.89
An enriched structural kinase database to enable kinome-wide structure-based analyses and drug discovery. Protein Sci (2010) 0.88
Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules. J Chem Inf Model (2013) 0.87
AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins. J Chem Inf Model (2014) 0.87
Energy landscape of chelated uranyl: antibody interactions by dynamic force spectroscopy. Biophys J (2007) 0.86
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Res (2014) 0.84
Structural properties of non-traditional drug targets present new challenges for virtual screening. J Chem Inf Model (2013) 0.83
Chemogenomic analysis of G-protein coupled receptors and their ligands deciphers locks and keys governing diverse aspects of signalling. PLoS One (2011) 0.81
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des (2012) 0.81
Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des (2015) 0.81
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PLoS Comput Biol (2013) 0.80
Biophysical limits of protein-ligand binding. J Chem Inf Model (2012) 0.79
Computational molecular modeling for evaluating the toxicity of environmental chemicals: prioritizing bioassay requirements. Environ Health Perspect (2008) 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
Ligand Identification Scoring Algorithm (LISA). J Chem Inf Model (2011) 0.79
Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case. Biopolymers (2016) 0.79
Discovering rules for protein-ligand specificity using support vector inductive logic programming. Protein Eng Des Sel (2009) 0.77
The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophys J (2006) 0.77
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. Database (Oxford) (2016) 0.76
Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J Chem Inf Model (2015) 0.76
Four-body atomic potential for modeling protein-ligand binding affinity: application to enzyme-inhibitor binding energy prediction. BMC Struct Biol (2013) 0.75
Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces. PLoS One (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
Fragment oriented molecular shapes. J Mol Graph Model (2016) 0.75
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge. J Comput Aided Mol Des (2016) 0.75
Prediction of kinase-inhibitor binding affinity using energetic parameters. Bioinformation (2016) 0.75
Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. J Comput Aided Mol Des (2017) 0.75
Testing the sensitivities of noncognate inhibitors to varicella zoster virus thymidine kinase: implications for postherpetic neuralgia therapy with existing agents. J Mol Model (2014) 0.75
Identification of proteins in human cytomegalovirus (HCMV) particles: the HCMV proteome. J Virol (2004) 4.30
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J Proteome Res (2005) 4.13
Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev (2006) 3.80
Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics (2002) 3.57
DAnTE: a statistical tool for quantitative analysis of -omics data. Bioinformatics (2008) 3.51
Comparative analysis of proteome and transcriptome variation in mouse. PLoS Genet (2011) 3.23
How much will Herceptin really cost? BMJ (2006) 3.23
Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry. Anal Chem (2006) 3.22
VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics (2007) 3.15
Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags. Proc Natl Acad Sci U S A (2002) 3.15
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res (2006) 3.10
High-sensitivity ion mobility spectrometry/mass spectrometry using electrodynamic ion funnel interfaces. Anal Chem (2005) 2.99
An IMS-IMS analogue of MS-MS. Anal Chem (2006) 2.68
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics (2009) 2.65
Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Mol Cell Proteomics (2005) 2.50
Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. PLoS Pathog (2010) 2.48
Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics (2011) 2.44
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol (2010) 2.41
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics (2008) 2.38
Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Anal Chem (2007) 2.38
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. J Proteome Res (2005) 2.35
Development of polyphosphate parameters for use with the AMBER force field. J Comput Chem (2003) 2.33
Integrative analysis of the mitochondrial proteome in yeast. PLoS Biol (2004) 2.31
Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Anal Chem (2005) 2.29
High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics (2006) 2.25
High-resolution field asymmetric waveform ion mobility spectrometry using new planar geometry analyzers. Anal Chem (2006) 2.19
Toward plasma proteome profiling with ion mobility-mass spectrometry. J Proteome Res (2006) 2.18
Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics (2006) 2.14
Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J (2008) 2.11
Evaluation of multiprotein immunoaffinity subtraction for plasma proteomics and candidate biomarker discovery using mass spectrometry. Mol Cell Proteomics (2006) 2.11
Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Mol Cell Proteomics (2008) 2.08
A statistical framework for protein quantitation in bottom-up MS-based proteomics. Bioinformatics (2009) 2.07
Development and evaluation of a micro- and nanoscale proteomic sample preparation method. J Proteome Res (2005) 2.06
The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle. Proc Natl Acad Sci U S A (2008) 2.05
Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface. J Am Soc Mass Spectrom (2007) 2.03
Fundamentals of traveling wave ion mobility spectrometry. Anal Chem (2008) 2.02
Clinical microfluidics for neutrophil genomics and proteomics. Nat Med (2010) 2.02
Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. Anal Chem (2003) 2.00
Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome. Anal Chem (2004) 2.00
High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology. Anal Chem (2004) 1.99
Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Res (2007) 1.99
Head-to-head comparison of serum fractionation techniques. J Proteome Res (2007) 1.98
Clustering millions of tandem mass spectra. J Proteome Res (2007) 1.98
Utilizing human blood plasma for proteomic biomarker discovery. J Proteome Res (2005) 1.96
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods (2011) 1.95
Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry. Proteomics (2005) 1.94
High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics (2004) 1.94
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A (2005) 1.93
Ion mobility spectrometry-mass spectrometry performance using electrodynamic ion funnels and elevated drift gas pressures. J Am Soc Mass Spectrom (2007) 1.93
Characterization of the mouse brain proteome using global proteomic analysis complemented with cysteinyl-peptide enrichment. J Proteome Res (2006) 1.93
Proteomics by FTICR mass spectrometry: top down and bottom up. Mass Spectrom Rev (2005) 1.91
Chemical screens against a reconstituted multiprotein complex: myricetin blocks DnaJ regulation of DnaK through an allosteric mechanism. Chem Biol (2011) 1.89
Ion funnel trap interface for orthogonal time-of-flight mass spectrometry. Anal Chem (2007) 1.88
High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem (2002) 1.88
Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics. Anal Chem (2005) 1.87
Precautionary behavior in response to perceived threat of pandemic influenza. Emerg Infect Dis (2007) 1.84
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal Chem (2006) 1.83
Analysis of the Salmonella typhimurium proteome through environmental response toward infectious conditions. Mol Cell Proteomics (2006) 1.82
Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation. Hepatology (2012) 1.82
Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface. J Am Soc Mass Spectrom (2006) 1.80
Proteomic analyses using an accurate mass and time tag strategy. Biotechniques (2004) 1.80
PRISM: a data management system for high-throughput proteomics. Proteomics (2006) 1.80
Does trypsin cut before proline? J Proteome Res (2007) 1.79
Enhanced ion utilization efficiency using an electrodynamic ion funnel trap as an injection mechanism for ion mobility spectrometry. Anal Chem (2008) 1.79
Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets. Proc Natl Acad Sci U S A (2012) 1.75
Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC/FTICR. Proc Natl Acad Sci U S A (2002) 1.72
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res (2008) 1.68
An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J Am Soc Mass Spectrom (2004) 1.68
Home-based medication review in older people: is it cost effective? Pharmacoeconomics (2007) 1.67
Ultrasensitive proteomics using high-efficiency on-line micro-SPE-nanoLC-nanoESI MS and MS/MS. Anal Chem (2004) 1.66
Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J Am Soc Mass Spectrom (2004) 1.66
Disclosure of genetic tests for health insurance: is it ethical not to? Lancet (2004) 1.65
Two-dimensional gas-phase separations coupled to mass spectrometry for analysis of complex mixtures. Anal Chem (2005) 1.65
Assessing quality of life in the elderly: a direct comparison of the EQ-5D and AQoL. Health Econ (2004) 1.64
Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic (2008) 1.63
CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J Chem Inf Model (2011) 1.61
MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features. Comput Biol Chem (2008) 1.61
Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J Am Soc Mass Spectrom (2003) 1.59
Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal Chem (2006) 1.59
In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun (2012) 1.58
Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS One (2009) 1.58
Paying for statins. BMJ (2004) 1.57
Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J Proteome Res (2004) 1.56
Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem (2006) 1.55
Establishing the proteome of normal human cerebrospinal fluid. PLoS One (2010) 1.53
Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proc Natl Acad Sci U S A (2012) 1.52
The ion funnel: theory, implementations, and applications. Mass Spectrom Rev (2010) 1.52
Exploring experimental sources of multiple protein conformations in structure-based drug design. J Am Chem Soc (2007) 1.52
Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS. J Am Soc Mass Spectrom (2008) 1.52
Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry. J Proteome Res (2007) 1.52
Deletion of GPR40 impairs glucose-induced insulin secretion in vivo in mice without affecting intracellular fuel metabolism in islets. Diabetes (2009) 1.51
Protein identification using top-down. Mol Cell Proteomics (2011) 1.50
Solving the problem of antimicrobial resistance: is a global approach necessary? Drug Discov Today (2003) 1.50
Comparative bacterial proteomics: analysis of the core genome concept. PLoS One (2008) 1.49
Understanding and designing field asymmetric waveform ion mobility spectrometry separations in gas mixtures. Anal Chem (2004) 1.48
Human cytomegalovirus UL97 kinase activity is required for the hyperphosphorylation of retinoblastoma protein and inhibits the formation of nuclear aggresomes. J Virol (2008) 1.48