Bibliography
- Terstappen GC, Reggiani A. In silico research in drug discovery. Trends Pharmacol Sci 2001;22:23-6
- Brass AL, Dykxhoorn DM, Benita Y, Identification of host proteins required for HIV infection through a functional genomic screen. Science 2008;319:921-6
- Dias R, de Azevedo WF Jr. Molecular docking algorithms. Curr Drug Targets 2008;9:1040-7
- Dror O, Shulman-Peleg A, Nussinov R, Wolfson HJ. Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. Curr Med Chem 2004;11:71-90
- Wolber G, Langer T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model 2005;45:160-9
- Steindl TM, Schuster D, Wolber G, High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening. J Comput Aided Mol Des 2006;20:703-15
- Kirchmair J, Ristic S, Eder K, Fast and efficient in silico 3D screening: toward maximum computational efficiency of pharmacophore-based and shape-based approaches. J Chem Inf Model 2007;47:2182-96
- Wolber G, Seidel T, Bendix F, Langer T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug Discov Today 2008;13:23-9
- Tintori C, Corradi V, Magnani M, Targets looking for drugs: a multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery. J Chem Inf Model 2008;48:2166-79
- Gedeck P, Lewis R. Exploiting QSAR models in lead optimization. Curr Opin Drug Discov Devel 2008;11:569-75
- Kirchmair J, Distinto S, Schuster D, Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates. Curr Med Chem 2008;15:2040-53
- Kirchmair J, Markt P, Distinto S, Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection–what can we learn from earlier mistakes? J Comput Aided Mol Des 2008;22:213-28
- Schnur DM. Recent trends in library design: 'rational design' revisited. Curr Opin Drug Discov Devel 2008;11:375-80
- Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 2009;19:120-7
- Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc 2002;124:5632-3
- Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. Discovering high-affinity ligands for proteins: SAR by NMR. Science 1996;274:1531-4
- Sherman W, Day T, Jacobson MP, Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49:534-54
- Sherman W, Beard HS, Farid R. Use of an induced fit receptor structure in virtual screening. Chem Biol Drug Des 2006;67:83-4
- Northrup SH, Erickson HP. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc Natl Acad Sci USA 1992;89:3338-42
- Wade RC, Gabdoulline RR, Lüdemann SK, Lounnas V. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. Proc Natl Acad Sci USA 1998;95:5942-9
- Veljkovic V. A theoretical approach to preselection of carcinogens and chemical carcinogenesis. Gordon & Breach; New York: 1980
- Veljkovic V, Slavic I. Simple general-model pseudopotential. Phys Rev Lett 1972;29:105-7
- Veljkovic V. The dependence of the Fermi energy on the atomic number. Phys Lett 1973;45A:41-2
- Todeschini R, Consoni V. Molecular descriptors for chemoinformatics. Wiley VCH Verlag; Weinheim: 2009
- Veljkovic V, Veljkovic N, Este JA, Application of the EIIP/ISM bioinformatics concept in development of new drugs. Curr Med Chem 2007;14:441-53
- Veljkovic N, Glisic S, Perovic V, Veljkovic V. The role of long-range intermolecular interactions in discovery of new drugs. Expert Opin Drug Discov 2011;6:1263-70
- Bolton E, Wang Y, Thiessen PA, Bryant SH. PubChem: integrated platform of small molecules and biological activities. Chapter 12. In: Annual reports in computational chemistry. Volume 4 American Chemical Society; Washington DC: 2008. Available from: http://www.ncbi.nlm.nih.gov/pccompound
- Veljkovic N, Glisic S, Prljic J, Simple and general criterion for “in silico” screening of candidate HIV drugs. Curr Pharm Biotechn 2012; Epub ahead of print CPB-EPUB-20120601-1
- Veljkovic V, Mouscadet JF, Veljkovic N, Simple criterion for selection of flavonoid compounds with anti-HIV activity. Bioorg Med Chem Lett 2007;17:1226-32
- Tintori C, Manetti F, Veljkovic N, Novel virtual screening protocol based on the combined use of molecular modeling and electron-ion interaction potential techniques to design HIV-1 integrase inhibitors. Chem Inf Model 2007;47:1536-44
- Mugnaini C, Rajamaki S, Tintori C, Toward novel HIV-1 integrase binding inhibitors: molecular modeling, synthesis, and biological studies. Bioorg Med Chem Lett 2007;17:5370-3
- Division of AIDS Anti-HIV/OI/TB Therapeutics Database. National Institutes of Health, U.S. Department of Health and Human Services. Available from: http://chemdb.niaid.nih.gov/AboutChemDB.aspx
- Spence RA, Kati WM, Anderson KS, Johnson KA. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Science 1995;267:988-93
- Spence RA, Anderson KS, Johnson KA. HIV-1 reverse transcriptase resistance to nonnucleoside inhibitors. Biochemistry 1996;35:1054-63
- Maga G, Amacker M, Ruel N, Resistance to nevirapine of HIV-1 reverse transcriptase mutants: loss of stabilizing interactions and thermodynamic or steric barriers are induced by different single amino acid substitutions. J Mol Biol 1997;274:738-47
- Maga G, Spadari S. Combinations against combinations: associations of anti-HIV 1 reverse transcriptase drugs challenged by constellations of drug resistance mutations. Curr Drug Metab 2002;3:73-95
- Basavapathruni A, Vingerhoets J, de Bethune MP, Modulation of human immunodeficiency virus type 1 synergistic inhibition by reverse transcriptase mutations. Iochemistry 2006;45:7334-40
- Xia Q, Radzio J, Anderson KS, Sluis-Cremer N. Probing nonnucleoside inhibitor-induced active-site distortion in HIV-1 reverse transcriptase by transient kinetic analyses. Protein Sci 2007;16:1728-37
- Lin LP, Huang LS, Lin CW, Determination of binding constant of DNA-binding drug to target DNA by surface plasmon resonance biosensor technology. Curr Drug Targets Immune Endocr Metabol Disord 2005;5:61-72
- Besenicar M, Macek P, Lakey JH, Anderluh G. Surface plasmon resonance in protein-membrane interactions. Chem Phys Lipids 2006;141:169-78
- Lausted C, Hu Z, Hood L, Campbell CT. SPR imaging for high throughput, label-free interaction analysis. Comb Chem High Throughput Screen 2009;12:741-51
- Marshall GR. Limiting assumptions in structure-based design: binding entropy. J Comput Aided Mol Des 2012;26:3-8
- Caporuscio F, Tafi A. Pharmacophore modelling: a forty year old approach and its modern synergies. Curr Med Chem 2011;18:2543-53
- McCammon JA. Target flexibility in molecular recognition. Biochim Biophys Acta 2005;1754:221-4
- Velazquez-Campoy A, Freire E. Incorporating target heterogeneity in drug design. J Cell Biochem Suppl 2001(Suppl 37):82-8
- Velazquez-Campoy A, Muzammil S, Ohtaka H, Structural and thermodynamic basis of resistance to HIV-1 protease inhibition: implications for inhibitor design. Curr Drug Targets Infect Disord 2003;3(4):311-28
- Freyer MW, Lewis EA. Isothermal titration calorimetry: experimental design, data analysis, and probing macromolecule/ligand binding and kinetic interactions. Methods Cell Biol 2008;84:79-113
- Liang Y. Applications of isothermal titration calorimetry in protein science. Acta Biochim Biophys Sin (Shanghai) 2008;40:565-76
- Knox RS. Forster's resonance excitation transfer theory: not just a formula. J Biomed Opt 2012;17:011003
- Lohse MJ, Hoffmann C, Nikolaev VO, Kinetic analysis of G protein-coupled receptor signaling using fluorescence resonance energy transfer in living cells. Adv Protein Chem 2007;74:167-88
- Grum-Tokars V, Ratia K, Begaye A, Evaluating the 3C-like protease activity of SARS-Coronavirus: recommendations for standardized assays for drug discovery. Virus Res 2008;133:63-73
- Tatham MH Hay RT. FRET-based in vitro assays for the analysis of SUMO protease activities. Methods Mol Biol 2009;497:253-68
- Degorce F, Card A, Soh S, HTRF: a technology tailored for drug discovery - a review of theoretical aspects and recent applications. Curr Chem Genomics 2009;3:22-32
- Mancini F, De Simone A, Andrisano V. Beta-secretase as a target for Alzheimer's disease drug discovery: an overview of in vitro methods for characterization of inhibitors. Anal Bioanal Chem 2011;400:1979-96
- Smiley RD, Hammes GG. Single molecule studies of enzyme mechanisms. Chem Rev 2006;106:3080-94
- Blank K, De Cremer G, Hofkens J. Fluorescence-based analysis of enzymes at the single-molecule level. Biotechnol J 2009;4:465-79
- Rissin DM, Gorris HH, Walt DR. Distinct and long-lived activity states of single enzyme molecules. J Am Chem Soc 2008;130:5349-53
- Gorris HH, Rissin DM, Walt DR. Stochastic inhibitor release and binding from single-enzyme molecules. Proc Natl Acad Sci USA 2007;104:17680-5
- Wallrabe H, Periasamy A. Imaging protein molecules using FRET and FLIM microscopy. Curr Opin Biotechnol 2005;16:19-27
- Sun Y, Wallrabe H, Seo SA, Periasamy A. FRET microscopy in 2010: the legacy of Theodor Forster on the 100th anniversary of his birth. ChemPhysChem 2010;12:462-74
- Stepanenko OV, Verkhusha VV, Kuznetsova IM, Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes. Curr Protein Pept Sci 2008;9:338-69
- Stepanenko OV, Shcherbakova DM, Kuznetsova IM, Modern fluorescent proteins: from chromophore formation to novel intracellular applications. Biotechniques 2011;51:313-14. 316,318 passim
- Kovarik ML, Allbritton NL. Measuring enzyme activity in single cells. Trends Biotechnol 2011;29:222-30
- He M, Edgar JS, Jeffries GD, Selective encapsulation of single cells and subcellular organelles into picoliter- and femtoliter-volume droplets. Anal Chem 2005;77:1539-44
- Baret JC, Miller OJ, Taly V, Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity. Lab Chip 2009;9:1850-8
- El-Ali J, Sorger PK, Jensen KF. Cells on chips. Nature 2006;442:403-11
- Di Carlo D, Aghdam N, Lee LP. Single-cell enzyme concentrations, kinetics, and inhibition analysis using high-density hydrodynamic cell isolation arrays. Anal Chem 2006;78:4925-30
- Di Carlo D, Wu LY, Lee LP. Dynamic single cell culture array. Lab Chip 2006;6:1445-9
- Xue Q, Yeung ES. Variability of intracellular lactate dehydrogenase isoenzymes in single human erythrocytes. Anal Chem 1994;66:1175-8
- Meredith GD, Sims CE, Soughayer JS, Allbritton NL. Measurement of kinase activation in single mammalian cells. Nat Biotechnol 2000;18:309-12
- Jiang D, Sims CE, Allbritton NL. Single-cell analysis of phosphoinositide 3-kinase and phosphatase and tensin homolog activation. Faraday Discuss 2011;149:187-200. discussion 227-45
- Krylov SN, Zhang Z, Chan NW, Correlating cell cycle with metabolism in single cells: combination of image and metabolic cytometry. Cytometry 1999;37:14-20
- Krylov SN, Arriaga EA, Chan NW, Metabolic cytometry: monitoring oligosaccharide biosynthesis in single cells by capillary electrophoresis. Anal Biochem 2000;283:133-5
- Radi M, Falchi F, Garbelli A, Discovery of the first small molecule inhibitor of human DDX3 specifically designed to target the RNA binding site: towards the next generation HIV-1 inhibitors. Bioorg Med Chem Lett 2012;22:2094-8
- Maga G, Falchi F, Garbelli A, Pharmacophore modeling and molecular docking led to the discovery of inhibitors of human immunodeficiency virus-1 replication targeting the human cellular aspartic acid-glutamic acid-alanine-aspartic acid box polypeptide 3. J Med Chem 2008;5:6635-8
- Radi M, Falciani C, Contemori L, A multidisciplinary approach for the identification of novel HIV-1 non-nucleoside reverse transcriptase inhibitors: S-DABOCs and DAVPs. ChemMedChem 2008;3:573-93
- Barreca ML, De Luca L, Iraci N, Structure-based pharmacophore identification of new chemical scaffolds as non-nucleoside reverse transcriptase inhibitors. J Chem Inf Model 2007;47:557-62
- Manetti F, Locatelli GA, Maga G, A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors. J Med Chem 2006;49:3278-86
- Fattorusso C, Gemma S, Butini S, Specific targeting highly conserved residues in the HIV-1 reverse transcriptase primer grip region. Design, synthesis, and biological evaluation of novel, potent, and broad spectrum NNRTIs with antiviral activity. J Med Chem 2005;48:7153-65
- Ingale KB, Bhatia MS. HIV-1 integrase inhibitors: a review of their chemical development. Antivir Chem Chemother 2011;22:95-105
- Vangelista L, Secchi M, Lusso P. Rational design of novel HIV-1 entry inhibitors by RANTES engineering. Vaccine 2008;26:3008-15