Published in PLoS Negl Trop Dis on August 24, 2010
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
Computational methods in drug discovery. Pharmacol Rev (2013) 1.51
Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des (2011) 1.13
BINANA: a novel algorithm for ligand-binding characterization. J Mol Graph Model (2011) 1.12
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput (2014) 1.08
Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei. RNA (2012) 0.97
HBonanza: a computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J Mol Graph Model (2011) 0.90
Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des (2013) 0.89
Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. J Biol Chem (2011) 0.87
The double-edged sword in pathogenic trypanosomatids: the pivotal role of mitochondria in oxidative stress and bioenergetics. Biomed Res Int (2014) 0.85
Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem (2012) 0.83
AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. J Mol Graph Model (2013) 0.82
Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3'-OH base mispairs and damaged base lesions. RNA (2013) 0.82
Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des (2014) 0.81
AutoClickChem: click chemistry in silico. PLoS Comput Biol (2012) 0.81
Inhibitors of RNA editing as potential chemotherapeutics against trypanosomatid pathogens. Int J Parasitol Drugs Drug Resist (2011) 0.81
Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. J Chem Inf Model (2013) 0.80
Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds. J Struct Biol (2012) 0.78
Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors. BMC Pharmacol (2011) 0.78
Novel cruzain inhibitors for the treatment of Chagas' disease. Chem Biol Drug Des (2012) 0.78
LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders. Chem Biol Drug Des (2012) 0.77
Charge reduction and thermodynamic stabilization of substrate RNAs inhibit RNA editing. PLoS One (2015) 0.76
Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J Chem Inf Model (2016) 0.76
CrystalDock: a novel approach to fragment-based drug design. J Chem Inf Model (2011) 0.76
RNA editing and drug discovery for cancer therapy. ScientificWorldJournal (2013) 0.75
Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. J Chem Inf Model (2016) 0.75
A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases. Nucleic Acids Res (2015) 0.75
Scalable molecular dynamics with NAMD. J Comput Chem (2005) 59.49
ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model (2005) 16.75
Control of neglected tropical diseases. N Engl J Med (2007) 14.49
Development and validation of a genetic algorithm for flexible docking. J Mol Biol (1997) 14.36
A fast flexible docking method using an incremental construction algorithm. J Mol Biol (1996) 7.33
The Alamar Blue assay to determine drug sensitivity of African trypanosomes (T.b. rhodesiense and T.b. gambiense) in vitro. Acta Trop (1997) 4.73
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des (2001) 4.54
Treatment of human African trypanosomiasis--present situation and needs for research and development. Lancet Infect Dis (2002) 3.73
Complex management: RNA editing in trypanosomes. Trends Biochem Sci (2005) 3.69
An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei. Science (2001) 3.52
The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem (2005) 3.36
Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29
A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J Comb Chem (1999) 3.09
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics (2009) 3.00
Human African trypanosomiasis: pharmacological re-engagement with a neglected disease. Br J Pharmacol (2007) 2.96
N-myristoyltransferase inhibitors as new leads to treat sleeping sickness. Nature (2010) 2.90
The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struct Biol (2004) 2.69
Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins (1999) 2.25
On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev (2003) 2.22
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei. RNA (2001) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
The two RNA ligases of the Trypanosoma brucei RNA editing complex: cloning the essential band IV gene and identifying the band V gene. Mol Cell Biol (2001) 2.05
Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr Genet (2005) 2.01
Human African trypanosomiasis: an emerging public health crisis. Br Med Bull (1998) 2.01
Uridine insertion/deletion RNA editing in trypanosome mitochondria: a complex business. RNA (2003) 1.85
Human African trypanosomiasis. BMJ (2002) 1.79
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
High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J Mol Biol (2004) 1.67
Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. J Med Chem (2007) 1.63
FEP-guided selection of bicyclic heterocycles in lead optimization for non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Am Chem Soc (2006) 1.36
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des (2009) 1.30
Pharmacokinetic investigations in patients from northern Angola refractory to melarsoprol treatment. Trop Med Int Health (2001) 1.21
Molecular mechanisms and therapeutic approaches to the treatment of African trypanosomiasis. Annu Rev Pharmacol Toxicol (1995) 1.13
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins (2004) 1.11
Simulations of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens. J Med Chem (2000) 1.00
The uptake of the trypanocidal drug suramin in combination with low-density lipoproteins by Trypanosoma brucei and its possible mode of action. Acta Trop (1993) 0.99
Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei. PLoS Negl Trop Dis (2007) 0.99
Uptake of the trypanocidal drug suramin by bloodstream forms of Trypanosoma brucei and its effect on respiration and growth rate in vivo. Mol Biochem Parasitol (1980) 0.98
Algorithms for computational solvent mapping of proteins. Proteins (2003) 0.97
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov (2009) 0.82
Toward understanding the conformational dynamics of RNA ligation. Biochemistry (2009) 0.81
Complex management: RNA editing in trypanosomes. Trends Biochem Sci (2005) 3.69
Identification of novel components of Trypanosoma brucei editosomes. RNA (2003) 2.30
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
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
High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1. J Mol Biol (2004) 1.67
Genetic dissection of a blood pressure quantitative trait locus on rat chromosome 1 and gene expression analysis identifies SPON1 as a novel candidate hypertension gene. Circ Res (2007) 1.53
Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res (2003) 1.52
Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun (2011) 1.39
Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res (2003) 1.29
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol (2009) 1.27
Glucose is toxic to glycosome-deficient trypanosomes. Proc Natl Acad Sci U S A (2002) 1.25
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. Nat Commun (2013) 1.21
A genome-wide survey demonstrates widespread non-linear mRNA in expressed sequences from multiple species. Nucleic Acids Res (2005) 1.20
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology. PLoS Comput Biol (2010) 1.19
KREPA6 is an RNA-binding protein essential for editosome integrity and survival of Trypanosoma brucei. RNA (2007) 1.14
The F(0)F(1)-ATP synthase complex contains novel subunits and is essential for procyclic Trypanosoma brucei. PLoS Pathog (2009) 1.14
The 14-3-3 proteins of Trypanosoma brucei function in motility, cytokinesis, and cell cycle. J Biol Chem (2005) 1.13
Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase. Biochemistry (2005) 1.12
Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput (2012) 1.11
An essential role of KREPB4 in RNA editing and structural integrity of the editosome in Trypanosoma brucei. RNA (2007) 1.08
Isolation and compositional analysis of trypanosomatid editosomes. Methods Enzymol (2007) 1.03
Identification and characterization of trypanosome RNA-editing complex components. Methods Mol Biol (2004) 1.02
AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des (2009) 1.01
Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei. PLoS Negl Trop Dis (2007) 0.99
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface. J Chem Theory Comput (2009) 0.98
The local dinucleotide preference of APOBEC3G can be altered from 5'-CC to 5'-TC by a single amino acid substitution. J Mol Biol (2013) 0.97
Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective. J Am Chem Soc (2009) 0.97
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics. J Comput Chem (2009) 0.96
A low-background inducible promoter system in Leishmania donovani. Mol Biochem Parasitol (2002) 0.91
Role of secondary sialic acid binding sites in influenza N1 neuraminidase. J Am Chem Soc (2010) 0.91
Mutational analysis of Trypanosoma brucei editosome proteins KREPB4 and KREPB5 reveals domains critical for function. RNA (2012) 0.90
Enigmatic presence of mitochondrial complex I in Trypanosoma brucei bloodstream forms. Eukaryot Cell (2011) 0.88
Evolution of dyskinetoplastic trypanosomes: how, and how often? Trends Parasitol (2010) 0.87
Biochemical, structural and molecular dynamics analyses of the potential virulence factor RipA from Yersinia pestis. PLoS One (2011) 0.87
Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds. PLoS One (2012) 0.86
Editosome accessory factors KREPB9 and KREPB10 in Trypanosoma brucei. Eukaryot Cell (2012) 0.85
Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. Proc Natl Acad Sci U S A (2011) 0.85
A potent, selective and cell-active allosteric inhibitor of protein arginine methyltransferase 3 (PRMT3). Angew Chem Int Ed Engl (2015) 0.85
Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR? Chem Biol Drug Des (2013) 0.85
Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. J Chem Inf Model (2012) 0.85
Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background. BMC Genomics (2010) 0.83
Rational prediction with molecular dynamics for hit identification. Curr Top Med Chem (2012) 0.83
Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. PLoS Comput Biol (2011) 0.82
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov (2009) 0.82
Computer-aided discovery of Trypanosoma brucei RNA-editing terminal uridylyl transferase 2 inhibitors. Chem Biol Drug Des (2014) 0.81
Toward understanding the conformational dynamics of RNA ligation. Biochemistry (2009) 0.81
Machine-learning techniques applied to antibacterial drug discovery. Chem Biol Drug Des (2015) 0.81
Multistructural hot spot characterization with FTProd. Bioinformatics (2012) 0.81
A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins. PLoS One (2013) 0.80
Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med (2012) 0.80
Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding. J Chem Inf Model (2013) 0.80
Independence from Kinetoplast DNA maintenance and expression is associated with multidrug resistance in Trypanosoma brucei in vitro. Antimicrob Agents Chemother (2014) 0.80
Molecular docking to flexible targets. Methods Mol Biol (2015) 0.79
Modeling the pharmacodynamics of passive membrane permeability. J Comput Aided Mol Des (2011) 0.78
How the ankyrin and SOCS box protein, ASB9, binds to creatine kinase. Biochemistry (2015) 0.78
Teach-Discover-Treat (TDT): collaborative computational drug discovery for neglected diseases. J Mol Graph Model (2012) 0.77
A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. J Chem Inf Model (2015) 0.77
38 Multiscale estimation of binding kinetics using molecular dynamics, brownian dynamics, and milestoning. J Biomol Struct Dyn (2015) 0.76
Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. Biochemistry (2012) 0.76
Trypanosoma brucei 14-3-3I and II proteins predominantly form a heterodimer structure that acts as a potent cell cycle regulator in vivo. J Biochem (2013) 0.75
Correction: TAC102 Is a Novel Component of the Mitochondrial Genome Segregation Machinery in Trypanosomes. PLoS Pathog (2016) 0.75
POVME 3.0: Software for Mapping Binding Pocket Flexibility. J Chem Theory Comput (2017) 0.75
Tribute to J. Andrew McCammon. J Phys Chem B (2016) 0.75
Designing novel inhibitors of Trypanosoma brucei. Methods Mol Biol (2013) 0.75
Erratum: Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein. Nat Microbiol (2017) 0.75
Computational chemistry and drug discovery: a call to action. Future Med Chem (2012) 0.75