Published in J Mol Graph Model on October 01, 2004
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci U S A (2009) 1.70
Conformational changes in protein loops and helices induced by post-translational phosphorylation. PLoS Comput Biol (2006) 1.36
Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations. PLoS Comput Biol (2009) 1.15
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases. Proteins (2009) 1.08
Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS Comput Biol (2011) 1.06
Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1. J Phys Chem B (2011) 0.97
Lck, Membrane Microdomains, and TCR Triggering Machinery: Defining the New Rules of Engagement. Front Immunol (2012) 0.85
Lck-dependent Fyn activation requires C terminus-dependent targeting of kinase-active Lck to lipid rafts. J Biol Chem (2008) 0.84
Technical phosphoproteomic and bioinformatic tools useful in cancer research. J Clin Bioinforma (2011) 0.83
Clinical proteomics and OMICS clues useful in translational medicine research. Proteome Sci (2012) 0.83
Hotspot mutations in KIT receptor differentially modulate its allosterically coupled conformational dynamics: impact on activation and drug sensitivity. PLoS Comput Biol (2014) 0.79
Loss of tyrosine phosphatase-dependent inhibition promotes activation of tyrosine kinase c-Src in detached pancreatic cells. Mol Carcinog (2010) 0.78
Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus. Appl Environ Microbiol (2007) 0.78
Cross-talk between nucleotide excision and homologous recombination DNA repair pathways in the mechanism of action of antitumor trabectedin. Cancer Res (2006) 1.94
Identification of the minimal conserved structure of HIV-1 protease in the presence and absence of drug pressure. AIDS (2004) 1.37
High sequence conservation of human immunodeficiency virus type 1 reverse transcriptase under drug pressure despite the continuous appearance of mutations. J Virol (2005) 1.24
The dual role of thymidine phosphorylase in cancer development and chemotherapy. Med Res Rev (2009) 1.22
Mutational pathways, resistance profile, and side effects of cyanovirin relative to human immunodeficiency virus type 1 strains with N-glycan deletions in their gp120 envelopes. J Virol (2006) 1.21
Development of a new family of conformationally restricted peptides as potent nucleators of beta-turns. Design, synthesis, structure, and biological evaluation of a beta-lactam peptide analogue of melanostatin. J Am Chem Soc (2003) 1.13
Molecular determinants of topoisomerase I poisoning by lamellarins: comparison with camptothecin and structure-activity relationships. J Med Chem (2005) 1.06
Molecular pharmacology and antitumor activity of Zalypsis in several human cancer cell lines. Biochem Pharmacol (2009) 1.06
Leishmania infantum expresses a mitochondrial nuclease homologous to EndoG that migrates to the nucleus in response to an apoptotic stimulus. Mol Biochem Parasitol (2008) 1.03
ET-18-OCH3 (edelfosine): a selective antitumour lipid targeting apoptosis through intracellular activation of Fas/CD95 death receptor. Curr Med Chem (2004) 1.01
Dimerization inhibitors of HIV-1 reverse transcriptase, protease and integrase: a single mode of inhibition for the three HIV enzymes? Antiviral Res (2006) 0.99
Antitumor activity, X-ray crystal structure, and DNA binding properties of thiocoraline A, a natural bisintercalating thiodepsipeptide. J Med Chem (2007) 0.95
Optimization of taxane binding to microtubules: binding affinity dissection and incremental construction of a high-affinity analog of paclitaxel. Chem Biol (2008) 0.95
HIV protease inhibition: limited recent progress and advances in understanding current pitfalls. Curr Top Med Chem (2004) 0.93
Structural basis for the binding of didemnins to human elongation factor eEF1A and rationale for the potent antitumor activity of these marine natural products. J Med Chem (2004) 0.92
XPF-dependent DNA breaks and RNA polymerase II arrest induced by antitumor DNA interstrand crosslinking-mimetic alkaloids. Chem Biol (2011) 0.91
The amino acid Asn136 in HIV-1 reverse transcriptase (RT) maintains efficient association of both RT subunits and enables the rational design of novel RT inhibitors. Mol Pharmacol (2005) 0.90
Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations. Nucleic Acids Res (2011) 0.89
Binding of 5'-GMP to the GluR2 AMPA receptor: insight from targeted molecular dynamics simulations. Biochemistry (2005) 0.88
Overcoming the inadequacies or limitations of experimental structures as drug targets by using computational modeling tools and molecular dynamics simulations. ChemMedChem (2007) 0.88
VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface. J Comput Aided Mol Des (2011) 0.88
3'-[4-Aryl-(1,2,3-triazol-1-yl)]-3'-deoxythymidine analogues as potent and selective inhibitors of human mitochondrial thymidine kinase. J Med Chem (2010) 0.87
Identification of aldo-keto reductase AKR1B10 as a selective target for modification and inhibition by prostaglandin A(1): implications for antitumoral activity. Cancer Res (2011) 0.87
The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulations. J Am Chem Soc (2005) 0.87
Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1. J Mol Biol (2003) 0.86
Tubulin-based structure-affinity relationships for antimitotic Vinca alkaloids. Anticancer Agents Med Chem (2012) 0.86
Relevance of the Fanconi anemia pathway in the response of human cells to trabectedin. Mol Cancer Ther (2008) 0.85
Synthesis, activity, and molecular modeling studies of novel human aldose reductase inhibitors based on a marine natural product. J Med Chem (2003) 0.85
Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry (2005) 0.85
Mitochondrial thymidine kinase inhibitors. Curr Top Med Chem (2005) 0.84
Antiviral agents: structural basis of action and rational design. Subcell Biochem (2013) 0.84
Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations. Nucleic Acids Res (2005) 0.84
The role of Thr139 in the human immunodeficiency virus type 1 reverse transcriptase sensitivity to (+)-calanolide A. Mol Pharmacol (2005) 0.83
Role of histidine-85 in the catalytic mechanism of thymidine phosphorylase as assessed by targeted molecular dynamics simulations and quantum mechanical calculations. Biochemistry (2004) 0.82
Recent advances in thymidine kinase 2 (TK2) inhibitors and new perspectives for potential applications. Curr Pharm Des (2012) 0.82
Exploring acyclic nucleoside analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase. ChemMedChem (2008) 0.81
Further insight into the DNA recognition mechanism of trabectedin from the differential affinity of its demethylated analogue ecteinascidin ET729 for the triplet DNA binding site CGA. J Med Chem (2006) 0.81
TSAO compounds: the comprehensive story of a unique family of HIV-1 specific inhibitors of reverse transcriptase. Curr Top Med Chem (2004) 0.81
Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity. Org Biomol Chem (2012) 0.81
Comparison of ultra-fast 2D and 3D ligand and target descriptors for side effect prediction and network analysis in polypharmacology. Br J Pharmacol (2013) 0.81
Molecular recognition of epothilones by microtubules and tubulin dimers revealed by biochemical and NMR approaches. ACS Chem Biol (2014) 0.80
Phosphorylation modulates the alpha-helical structure and polymerization of a peptide from the third tau microtubule-binding repeat. Biochim Biophys Acta (2004) 0.80
Structure, physiological role, and specific inhibitors of human thymidine kinase 2 (TK2): present and future. Med Res Rev (2008) 0.80
Synthesis, modeling and evaluation of 3'-(1-aryl-1H-tetrazol-5-ylamino)-substituted 3'-deoxythymidine derivatives as potent and selective human mitochondrial thymidine kinase inhibitors. Org Biomol Chem (2010) 0.80
Understanding the basis of resistance in the irksome Lys103Asn HIV-1 reverse transcriptase mutant through targeted molecular dynamics simulations. J Am Chem Soc (2004) 0.80
DNA structural similarity in the 2:1 complexes of the antitumor drugs trabectedin (Yondelis) and chromomycin A3 with an oligonucleotide sequence containing two adjacent TGG binding sites on opposing strands. Mol Pharmacol (2005) 0.79
Characterization of pyrimidine nucleoside phosphorylase of Mycoplasma hyorhinis: implications for the clinical efficacy of nucleoside analogues. Biochem J (2012) 0.79
Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. J Comput Aided Mol Des (2003) 0.79
Synthesis and biological evaluation of a new series of highly functionalized 7'-homo-anhydrovinblastine derivatives. J Med Chem (2013) 0.79
5'-Trityl-substituted thymidine derivatives as a novel class of antileishmanial agents: Leishmania infantum EndoG as a potential target. ChemMedChem (2013) 0.78
Solution structure and stability of tryptophan-containing nucleopeptide duplexes. Chembiochem (2003) 0.78
Stepwise dissection and visualization of the catalytic mechanism of haloalkane dehalogenase LinB using molecular dynamics simulations and computer graphics. J Mol Graph Model (2007) 0.78
Inhibitory effects of marine-derived DNA-binding anti-tumour tetrahydroisoquinolines on the Fanconi anaemia pathway. Br J Pharmacol (2013) 0.78
Guanidinium receptors as enantioselective amino acid membrane carriers. J Am Chem Soc (2003) 0.78
Human mitochondrial thymidine kinase is selectively inhibited by 3'-thiourea derivatives of beta-thymidine: identification of residues crucial for both inhibition and catalytic activity. Mol Pharmacol (2009) 0.78
A 3.(ET743)-DNA complex that both resembles an RNA-DNA hybrid and mimicks zinc finger-induced DNA structural distortions. J Med Chem (2002) 0.78
Improving the antiviral efficacy and selectivity of HIV-1 reverse transcriptase inhibitor TSAO-T by the introduction of functional groups at the N-3 position. J Med Chem (2005) 0.78
Mechanistic insight into the catalytic activity of ββα-metallonucleases from computer simulations: Vibrio vulnificus periplasmic nuclease as a test case. Chembiochem (2011) 0.77
Improving the selectivity of acyclic nucleoside analogues as inhibitors of human mitochondrial thymidine kinase: replacement of a triphenylmethoxy moiety with substituted amines and carboxamides. Bioorg Med Chem Lett (2003) 0.77
The Protein kinase inhibitor balanol: structure-activity relationships and structure-based computational studies. Anticancer Agents Med Chem (2008) 0.77
Comparative binding energy (COMBINE) analysis supports a proposal for the binding mode of epothilones to β-tubulin. ChemMedChem (2012) 0.76
Discovery of TSAO derivatives with an unusual HIV-1 activity/resistance profile. Antiviral Res (2006) 0.76
CRDOCK: an ultrafast multipurpose protein-ligand docking tool. J Chem Inf Model (2012) 0.76
Suppression of the acuH13 and acuH31 nonsense mutations in the carnitine/acylcarnitine translocase (acuH) gene of Aspergillus nidulans by the G265S substitution in the domain 2 of the release factor eRF1. Fungal Genet Biol (2006) 0.76
Understanding the key factors that control the inhibition of type II dehydroquinase by (2R)-2-benzyl-3-dehydroquinic acids. ChemMedChem (2010) 0.76
Modulation of binding strength in several classes of active site inhibitors of acetylcholinesterase studied by comparative binding energy analysis. J Med Chem (2004) 0.76
Probing the dimerization interface of Leishmania infantum trypanothione reductase with site-directed mutagenesis and short peptides. Chembiochem (2013) 0.76
ALFA: automatic ligand flexibility assignment. J Chem Inf Model (2014) 0.75
Chemometrical identification of mutations in HIV-1 reverse transcriptase conferring resistance or enhanced sensitivity to arylsulfonylbenzonitriles. J Am Chem Soc (2004) 0.75
gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Proteins (2010) 0.75
A reverse combination of structure-based and ligand-based strategies for virtual screening. J Comput Aided Mol Des (2012) 0.75
New horizons in pharmaceutical biotechnology by melding biology and engineering. Curr Opin Biotechnol (2013) 0.75
AtlasCBS: a web server to map and explore chemico-biological space. J Comput Aided Mol Des (2012) 0.75
A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure-activity relationships using comparative binding energy (COMBINE) analysis. Org Biomol Chem (2013) 0.75
N1-substituted thymine derivatives as mitochondrial thymidine kinase (TK-2) inhibitors. J Med Chem (2006) 0.75
Synthesis and structural characterization of pyrimidine bi- and tricyclic nucleosides with sugar puckers conformationally locked into the eastern region of the pseudorotational cycle. J Org Chem (2003) 0.75
Unusual approach to 3-aryl-2-aminopyridines through a radical mechanism: synthesis and theoretical rationale from quantum mechanical calculations. J Org Chem (2011) 0.75
Current perspective of information technologies in drug discovery. J Comput Aided Mol Des (2002) 0.75
In memoriam. Angel Ramírez Ortiz (1966-2008). Proteins (2010) 0.75
Diastereoselective reactions in glycine templates containing an ent-ardeemin fragment. J Org Chem (2002) 0.75
Benzo[f]azino[2,1-a]phthalazinium cations: novel DNA intercalating chromophores with antiproliferative activity. J Med Chem (2004) 0.75
One-pot synthesis of vinca alkaloids-phomopsin hybrids. J Med Chem (2014) 0.75
7,5'-O-dibenzylinosines: synthesis and studies on their conformational properties. Nucleosides Nucleotides Nucleic Acids (2007) 0.75
Intramolecular cation-pi interactions as the driving force to restrict the conformation of certain nucleosides. J Org Chem (2010) 0.75
Solution structure and stability of a disulfide cross-linked nucleopeptide duplex. Chem Commun (Camb) (2003) 0.75
Microwave-assisted synthesis of potent PDE7 inhibitors containing a thienopyrimidin-4-amine scaffold. Org Biomol Chem (2014) 0.75
Synthesis of 3' '-substituted TSAO derivatives with anti-HIV-1 and anti-HIV-2 activity through an efficient palladium-catalyzed cross-coupling approach. J Med Chem (2002) 0.75
A computational fragment-based de novo design protocol guided by ligand efficiency indices (LEI). Methods Mol Biol (2015) 0.75
Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem (2013) 0.75