Published in Bioinformatics on June 28, 2007
Open Babel: An open chemical toolbox. J Cheminform (2011) 11.12
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
ChemMine tools: an online service for analyzing and clustering small molecules. Nucleic Acids Res (2011) 1.56
Computational methods in drug discovery. Pharmacol Rev (2013) 1.51
Chemical databases for environmental health and clinical research. Toxicol Lett (2008) 1.15
Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. J Chem Inf Model (2011) 1.02
When is chemical similarity significant? The statistical distribution of chemical similarity scores and its extreme values. J Chem Inf Model (2010) 0.97
Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis. Proc Natl Acad Sci U S A (2012) 0.96
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. Nucleic Acids Res (2010) 0.96
MMsINC: a large-scale chemoinformatics database. Nucleic Acids Res (2008) 0.96
An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. J Biomol Screen (2014) 0.95
Inhibition of histo-blood group antigen binding as a novel strategy to block norovirus infections. PLoS One (2013) 0.86
No electron left behind: a rule-based expert system to predict chemical reactions and reaction mechanisms. J Chem Inf Model (2009) 0.85
An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databases. J Chem Inf Model (2009) 0.84
A multi-fingerprint browser for the ZINC database. Nucleic Acids Res (2014) 0.83
Hashing algorithms and data structures for rapid searches of fingerprint vectors. J Chem Inf Model (2010) 0.82
Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing. Bioinformatics (2010) 0.81
BLASTing small molecules--statistics and extreme statistics of chemical similarity scores. Bioinformatics (2008) 0.80
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. J Cheminform (2015) 0.79
Tyrosine aminotransferase from Leishmania infantum: A new drug target candidate. Int J Parasitol Drugs Drug Resist (2014) 0.78
Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics. Cancer Inform (2010) 0.75
An infrastructure to mine molecular descriptors for ligand selection on virtual screening. Biomed Res Int (2014) 0.75
An Effective Approach for Clustering InhA Molecular Dynamics Trajectory Using Substrate-Binding Cavity Features. PLoS One (2015) 0.75
Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins (2002) 5.29
An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res (2006) 4.51
The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A (2006) 4.18
Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci U S A (2005) 3.77
A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol Cell Proteomics (2006) 3.62
Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A (2005) 3.59
MITOMAP: a human mitochondrial genome database--2004 update. Nucleic Acids Res (2005) 3.35
Prediction of protein stability changes for single-site mutations using support vector machines. Proteins (2006) 3.00
A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc Natl Acad Sci U S A (2010) 2.90
Prediction of coordination number and relative solvent accessibility in proteins. Proteins (2002) 2.66
Profiling humoral immune responses to P. falciparum infection with protein microarrays. Proteomics (2008) 2.43
Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem (2003) 2.32
Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A (2012) 2.22
ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics (2005) 2.16
A genome-wide proteome array reveals a limited set of immunogens in natural infections of humans and white-footed mice with Borrelia burgdorferi. Infect Immun (2008) 2.15
A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci U S A (2009) 2.10
Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics (2007) 2.03
Data structures and compression algorithms for genomic sequence data. Bioinformatics (2009) 1.96
Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time. J Chem Inf Model (2007) 1.86
Bayesian surprise attracts human attention. Vision Res (2008) 1.86
Graph kernels for chemical informatics. Neural Netw (2005) 1.86
Immunodominant Francisella tularensis antigens identified using proteome microarray. Proteomics (2007) 1.85
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics (2008) 1.78
A machine learning information retrieval approach to protein fold recognition. Bioinformatics (2006) 1.75
MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics (2008) 1.73
Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem (2005) 1.73
Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J Biol Chem (2002) 1.69
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis. Bioinformatics (2007) 1.68
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques. Bioinformatics (2006) 1.65
Development of a novel cross-linking strategy for fast and accurate identification of cross-linked peptides of protein complexes. Mol Cell Proteomics (2010) 1.61
Cyber-T web server: differential analysis of high-throughput data. Nucleic Acids Res (2012) 1.58
COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel (2008) 1.54
Sterile protective immunity to malaria is associated with a panel of novel P. falciparum antigens. Mol Cell Proteomics (2011) 1.53
Abdominal insufflation decreases blood loss and mortality after porcine liver injury. J Trauma (2005) 1.47
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics (2005) 1.47
Deep architectures for protein contact map prediction. Bioinformatics (2012) 1.44
Differential analysis of DNA microarray gene expression data. Mol Microbiol (2003) 1.43
Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A (2006) 1.42
Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins (2006) 1.41
Assessment of predictions submitted for the CASP7 domain prediction category. Proteins (2007) 1.39
Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res (2005) 1.38
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat Neurosci (2013) 1.36
Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin. Cell Metab (2013) 1.32
Data structures and compression algorithms for high-throughput sequencing technologies. BMC Bioinformatics (2010) 1.31
Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics (2002) 1.25
The stability and complexity of antibody responses to the major surface antigen of Plasmodium falciparum are associated with age in a malaria endemic area. Mol Cell Proteomics (2011) 1.24
Why are complementary DNA strands symmetric? Bioinformatics (2002) 1.23
Calcium mediates bidirectional growth cone turning induced by myelin-associated glycoprotein. Neuron (2004) 1.20
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (2010) 1.20
A survey of current trends in computational drug repositioning. Brief Bioinform (2015) 1.18
Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics (2005) 1.16
Lossless compression of chemical fingerprints using integer entropy codes improves storage and retrieval. J Chem Inf Model (2007) 1.14
SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics (2009) 1.14
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. Nat Methods (2012) 1.14
LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res (2003) 1.14
Discovery of power-laws in chemical space. J Chem Inf Model (2008) 1.11
Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One (2011) 1.11
Circadian acetylome reveals regulation of mitochondrial metabolic pathways. Proc Natl Acad Sci U S A (2013) 1.11
Mapping the structural topology of the yeast 19S proteasomal regulatory particle using chemical cross-linking and probabilistic modeling. Mol Cell Proteomics (2012) 1.10
MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat (2009) 1.10
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinformatics (2011) 1.10
Small-molecule 3D structure prediction using open crystallography data. J Chem Inf Model (2013) 1.10
One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. J Chem Inf Model (2007) 1.09
Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis (2010) 1.08
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. Bioinformatics (2007) 1.07
SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct Biol (2008) 1.07
Circadian clock regulates the host response to Salmonella. Proc Natl Acad Sci U S A (2013) 1.07
Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules. J Chem Inf Model (2013) 1.07
Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors. PLoS Comput Biol (2010) 1.06
Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays. Vaccine (2009) 1.05
Ty3 capsid mutations reveal early and late functions of the amino-terminal domain. J Virol (2007) 1.03
Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. J Chem Inf Model (2011) 1.02
ICBS: a database of interactions between protein chains mediated by beta-sheet formation. Bioinformatics (2004) 1.02
The fixed-size Luria-Delbruck model with a nonzero death rate. Math Biosci (2007) 1.01
A WNT/p21 circuit directed by the C-clamp, a sequence-specific DNA binding domain in TCFs. Mol Cell Biol (2012) 1.00
Influence relevance voting: an accurate and interpretable virtual high throughput screening method. J Chem Inf Model (2009) 1.00
GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. PLoS Genet (2012) 0.99
The RhoGEF trio functions in sculpting class specific dendrite morphogenesis in Drosophila sensory neurons. PLoS One (2012) 0.99
Mitochondrial mutations and polymorphisms in psychiatric disorders. Front Genet (2012) 0.98
Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. Mol Cell Proteomics (2012) 0.98
High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics (2010) 0.97
Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. PLoS Pathog (2010) 0.96
Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol (2013) 0.96
Large scale study of multiple-molecule queries. J Cheminform (2009) 0.95
Cervical spine injury is highly dependent on the mechanism of injury following blunt and penetrating assault. J Trauma (2006) 0.93
Modular DAG-RNN architectures for assembling coarse protein structures. J Comput Biol (2006) 0.93
Mathematical correction for fingerprint similarity measures to improve chemical retrieval. J Chem Inf Model (2007) 0.93
Functional genomic analyses of two morphologically distinct classes of Drosophila sensory neurons: post-mitotic roles of transcription factors in dendritic patterning. PLoS One (2013) 0.93
Learning to predict chemical reactions. J Chem Inf Model (2011) 0.92
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proc Natl Acad Sci U S A (2010) 0.91
Identification of immunodominant antigens by probing a whole Chlamydia trachomatis open reading frame proteome microarray using sera from immunized mice. Infect Immun (2010) 0.90
Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants. IEEE/ACM Trans Comput Biol Bioinform (2006) 0.90
Retrotransposon profiling of RNA polymerase III initiation sites. Genome Res (2012) 0.90
The absence of favorable aromatic interactions between beta-sheet peptides. J Am Chem Soc (2005) 0.90