Publication list

publication_uri type publication_title year doi pmid journal_uri AcademicArticle Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket 2019 10.1128/mBio.02858-18 30862755 AcademicArticle Labels on levels: labeling of multi-scale multi-instance and crowded 3D biological environments 2019 10.1109/tvcg.2018.2864491 30130195 AcademicArticle Integrative modeling of the HIV-1 ribonucleoprotein complex 2019 10.1371/journal.pcbi.1007150 31194731 AcademicArticle RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy 2019 10.1093/nar/gky1004 30357411 AcademicArticle Late-onset retinal degeneration pathology due to mutations in CTRP5 is mediated through HTRA1 2019 10.1111/acel.13011 31385385 AcademicArticle CellPAINT: Interactive illustration of dynamic mesoscale cellular environments 2018 10.1109/mcg.2018.2877076 30668455 AcademicArticle Instant construction and visualization of crowded biological environments 2018 10.1109/tvcg.2017.2744258 28866533 AcademicArticle Lattice Models of Bacterial Nucleoids 2018 10.1021/acs.jpcb.7b11770 29338247 AcademicArticle From atoms to cells: using mesoscale landscapes to construct visual narratives 2018 10.1016/j.jmb.2018.06.009 29885327 AcademicArticle Molecular illustration in research and education: past, present, and future 2018 10.1016/j.jmb.2018.04.043 29752966 AcademicArticle The RCSB protein data bank: integrative view of protein, gene and 3D structural information 2017 10.1093/nar/gkw1000 27794042 AcademicArticle A visual review of the human pathogen Streptococcus pneumoniae 2017 10.1093/femsre/fux037 29029129 AcademicArticle Covalent docking using autodock: two-point attractor and flexible side chain methods 2016 10.1002/pro.2733 26103917 AcademicArticle RCSB Protein Data Bank: A resource for chemical, biochemical, and structural explorations of large and small biomolecules 2016 10.1021/acs.jchemed.5b00404 AcademicArticle Computational protein-ligand docking and virtual drug screening with the AutoDock suite 2016 10.1038/nprot.2016.051 27077332 AcademicArticle Fragment-based analysis of ligand dockings improves classification of actives 2016 10.1021/acs.jcim.6b00248 27384036 AcademicArticle Visibility equalizer cutaway visualization of mesoscopic biological models 2016 10.1111/cgf.12892 AcademicArticle cellPACK: a virtual mesoscope to model and visualize structural systems biology 2015 10.1038/nmeth.3204 25437435 Chapter Illustrations of the HIV Life Cycle 2015 10.1007/82_2015_437 AcademicArticle The RCSB PDB "molecule of the month": Inspiring a molecular view of biology 2015 10.1371/journal.pbio.1002140 25942442 AcademicArticle The RCSB Protein Data Bank: views of structural biology for basic and applied research and education 2015 10.1093/nar/gku1214 25428375 AcademicArticle AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility 2015 10.1371/journal.pcbi.1004586 26629955 EditedBook Future of HIV-1 therapeutics: resistance is futile? 2015 AcademicArticle Visualising microorganisms from molecules to cells 2014 10.1111/1574-6968.12485 25039917 AcademicArticle 3D molecular models of whole HIV-1 virions generated with cellPACK 2014 10.1039/c4fd00017j 25253262 AcademicArticle Protein structure in context: The molecular landscape of angiogenesis 2013 10.1002/bmb.20706 23868376 AcademicArticle The effects of the SUN project on teacher knowledge and self-efficacy regarding biological energy transfer are significant and long-lasting: results of a randomized controlled trial 2013 10.1187/cbe.12-09-0155 23737635 AcademicArticle Revealing structural views of biology 2013 10.1002/bip.22338 23821527 AcademicArticle The RCSB protein data bank: New resources for research and education 2013 10.1093/nar/gks1200 23193259 AcademicArticle Protein flexibility in virtual screening: the BACE-1 case study 2012 10.1021/ci300390h 23005250 AcademicArticle Putting proteins in context 2012 10.1002/bies.201200072 22806423 AcademicArticle Illustrating the machinery of life: Viruses 2012 10.1002/bmb.20636 22987549 AcademicArticle The RCSB protein data bank: Redesigned web site and web services 2011 10.1093/nar/gkq1021 21036868 AcademicArticle Redox-based probes for protein tyrosine phosphatases 2011 10.1002/anie.201007871 21504031 AcademicArticle The evolution of the RCSB Protein Data Bank website 2011 10.1002/wcms.57 AcademicArticle ePMV embeds molecular modeling into professional animation software environments 2011 10.1016/j.str.2010.12.023 21397181 AcademicArticle Miniseries: Illustrating the machineryof life: Eukaryotic cell panorama 2011 10.1002/bmb.20494 21445900 AcademicArticle Artophagy: the art of autophagy--the Cvt pathway 2010 10.4161/auto.6.1.10812 20023390 AcademicArticle Visualizing biological data: now and in the future 2010 10.1038/nmeth.f.301 20195254 AcademicArticle Visualization of macromolecular structures 2010 10.1038/nmeth.1427 20195256 AcademicArticle Mitochondrion 2010 10.1002/bmb.20406 21567815 AcademicArticle Virtual screening with AutoDock: theory and practice 2010 10.1517/17460441.2010.484460 21532931 AcademicArticle Promoting a structural view of biology for varied audiences: An overview of RCSB PDB resources and experiences 2010 10.1107/s002188981002371x 20877496 AcademicArticle Escherichia coli 2009 10.1002/bmb.20345 21567766 AcademicArticle Neuromuscular synapse 2009 10.1002/bmb.20297 21567738 AcademicArticle AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility 2009 10.1002/jcc.21256 19399780 AcademicArticle Automated prediction of ligand-binding sites in proteins 2008 10.1002/prot.21645 17910060 AcademicArticle Empirical entropic contributions in computational docking: evaluation in APS reductase complexes 2008 10.1002/jcc.20936 18351616 AcademicArticle Structure-based virtual screening and biological evaluation of Mycobacterium tuberculosis adenosine 5'-phosphosulfate reductase inhibitors 2008 10.1021/jm800571m 18855373 AcademicArticle Filling in the gaps: Artistic license in education and outreach 2007 10.1371/journal.pbio.0050308 18052608 AcademicArticle A semiempirical free energy force field with charge-based desolvation 2007 10.1002/jcc.20634 17274016 AcademicArticle The molecular perspective: Hepatitis b virus 2007 10.1634/theoncologist.12-5-516 17522238 AcademicArticle Recognition highlights: Toll-like receptors 2006 10.1002/jmr.778 16721899 AcademicArticle Seeing the nanoscale 2006 10.1016/s1748-0132(06)70079-2 AcademicArticle The molecular perspective: Alcohol 2006 10.1634/theoncologist.11-9-1045 17030647 AcademicArticle The molecular perspective: Cisplatin 2006 10.1634/theoncologist.11-3-316 16549816 AcademicArticle Tactile teaching - exploring protein structure/function using physical models 2006 10.1002/bmb.2006.494034042649 21638686 AcademicArticle The molecular perspective: Tumor necrosis factor 2006 10.1634/theoncologist.11-1-83 16401717 AcademicArticle The molecular perspective: Tissue factor 2006 10.1634/theoncologist.11-7-849 16880244 AcademicArticle The molecular perspective: Estrogen sulfotransferase 2006 10.1634/theoncologist.11-4-418 16614238 AcademicArticle The molecular perspective: Cisplatin 2006 10.1634/stemcells.2006-CSC2 16582013 AcademicArticle Identification of sanguinarine as a novel hiv protease inhibitor from high-throughput screening of 2,000 drugs and natural products with a cell-based assay 2005 10.2174/1570180054405811 AcademicArticle Visual methods from atoms to cells 2005 10.1016/j.str.2005.01.012 15766535 AcademicArticle The molecular perspective: Double-stranded DNA breaks 2005 10.1634/theoncologist.10-5-361 15851795 AcademicArticle 1,2,3-triazole as a peptide surrogate in the rapid synthesis of HIV-1 protease inhibitors 2005 10.1002/cbic.200500101 15934050 AcademicArticle Identifying protein binding sites and optimal ligands 2005 10.2174/1570180054771572 AcademicArticle The molecular perspective: Major histocompatibility complex 2005 10.1634/theoncologist.10-1-80 15632255 AcademicArticle The cAMP binding domain: An ancient signaling module 2005 10.1073/pnas.0408579102 15618393 Chapter Augmented reality with tangible auto-fabricated models for molecular biology applications 2004 10.1109/VISUAL.2004.7 Book Computer-linked autofabricated 3D models for teaching structural biology 2004 AcademicArticle Grid-based hydrogen bond potentials with improved directionality 2004 10.2174/1570180043485581 AcademicArticle The molecular perspective: Nicotine and nitrosamines 2004 10.1634/theoncologist.9-3-353 15169991 AcademicArticle The molecular perspective: Cytochrome C and apoptosis 2004 10.1634/theoncologist.9-2-226 15047927 AcademicArticle Bioeditor-simplifying macromolecular structure annotation 2003 10.1093/bioinformatics/btg103 12724304 AcademicArticle Rapid diversity-oriented synthesis in microtiter plates for in situ screening of HIV protease inhibitors 2003 10.1002/cbic.200300724 14613121 AcademicArticle The molecular perspective: Vegf and angiogenesis 2003 10.1634/stemcells.21-1-118 12529559 AcademicArticle The molecular perspective: Histone deacetylase 2003 10.1634/stemcells.21-5-620 12968116 AcademicArticle The molecular perspective: Epidermal growth factor 2003 10.1634/theoncologist.8-5-496 14530503 AcademicArticle Looking at molecules - an essay on art and science 2003 10.1002/cbic.200300747 14661269 AcademicArticle Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling 2003 10.1023/b:jcam.0000004604.87558.02 14703123 AcademicArticle Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock 2002 10.1002/prot.10028 11746701 AcademicArticle Evolutionary analysis of HIV-1 protease inhibitors: methods for design of inhibitors that evade resistance 2002 10.1002/prot.10130 12012338 AcademicArticle Protein structures: From famine to feast 2002 10.1511/2002.4.350 AcademicArticle The molecular perspective: Bcl-2 and apoptosis 2002 10.1634/theoncologist.7-3-259 12065800 AcademicArticle The molecular perspective: Tamoxifen and the estrogen receptor 2002 10.1634/stemcells.20-3-267 12004085 AcademicArticle The molecular perspective: Cadherin 2002 10.1634/theoncologist.7-5-467 12401910 AcademicArticle A study on docking mode of HIV protease and their inhibitors 2001 10.2477/jchemsoft.7.103 AcademicArticle Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation 2001 10.1002/prot.1038 11288177 AcademicArticle Sequence recognition of DNA by lexitropsins 2001 11281838 AcademicArticle The molecular perspective: Cytochrome P450 2001 10.1634/theoncologist.6-2-205 11306732 AcademicArticle The molecular perspective: The ribosome 2001 10.1111/0735-2751.00130 11209095 AcademicArticle Recognition templates for predicting adenylate-binding sites in proteins 2001 10.1006/jmbi.2001.5201 11743737 AcademicArticle The molecular perspective: Cytochrome P450 2001 10.1634/stemcells.19-3-263 11359952 AcademicArticle Protein-ligand docking 2000 10.1002/9783527613168.ch3 AcademicArticle Biomolecules and nanotechnology 2000 10.1511/2000.23.769 AcademicArticle The molecular perspective: DNA 2000 10.1634/stemcells.18-2-148 10742387 AcademicArticle The molecular perspective: Cyclooxygenase-2 2000 10.1634/stemcells.18-3-227 10840077 AcademicArticle The molecular perspective: Simian virus 40 [reprint] 2000 10.1634/stemcells.18-4-301 10924097 AcademicArticle Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism 2000 10.1002/1099-1352(200005/06)13:3<146::aid-jmr497>;2-4 10867710 AcademicArticle Structural symmetry and protein function 2000 10.1146/annurev.biophys.29.1.105 10940245 AcademicArticle The molecular perspective: Matrix metalloproteinase 2 2000 10.1634/stemcells.18-1-73 10661578 AcademicArticle The art of molecular graphics - escape from flatland 2000 10935209 AcademicArticle The molecular perspective: The ribosome 2000 10.1634/theoncologist.5-6-508 11110603 AcademicArticle The molecular perspective: Simian virus 40 2000 10.1634/theoncologist.5-3-260 10884504 AcademicArticle The molecular perspective: Cyclooxygenase-2 2000 10.1634/theoncologist.5-2-169 10794808 AcademicArticle The molecular perspective: DNA 2000 10.1634/theoncologist.5-1-81 10706655 AcademicArticle The molecular perspective: Microtubules and the taxanes 2000 10.1634/theoncologist.5-4-345 10965003 AcademicArticle The molecular perspective: Caspases 2000 10.1634/theoncologist.5-5-435 11040280 AcademicArticle The art of molecular graphics - jaggies begone! 1999 AcademicArticle Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors 1999 10.1006/jmbi.1998.2579 10074408 AcademicArticle The molecular perspective: The ras oncogene 1999 10437988 AcademicArticle The molecular perspective: Methotrexate 1999 10527466 AcademicArticle Where two worlds collide: Art meets science 1999 AcademicArticle The molecular perspective: P53 tumor suppressor 1999 10342561 AcademicArticle The molecular perspective: The multidrug transporter 1999 10606167 AcademicArticle Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease 1999 10.1073/pnas.96.4.1369 9990030 AcademicArticle Docking of 4-oxalocrotonate tautomerase substrates: implications for the catalytic mechanism 1999 10.1002/(sici)1097-0282(199909)50:3<319::aid-bip7>;2-8 10397792 AcademicArticle The molecular perspective: The multidrug transporter 1999 10551560 AcademicArticle The molecular perspective: Matrix metalloproteinase 2 1999 10631695 AcademicArticle The molecular perspective: P53 tumor suppressor 1999 10337384 AcademicArticle The molecular perspective: The ras oncogene 1999 10394594 AcademicArticle The molecular perspective: Methotrexate 1999 10476546 AcademicArticle Morphology of protein-protein interfaces 1998 10.1016/s0969-2126(98)00044-6 9562553 AcademicArticle Computational coevolution of antiviral drug resistance 1998 10.1162/106454698568431 9798274 AcademicArticle An analysis of a class of DNA sequence reading molecules 1998 10.1089/cmb.1998.5.571 9773351 AcademicArticle The theoretical limits of DNA sequence discrimination by linked polyamides 1998 10.1073/pnas.95.8.4315 9539734 AcademicArticle Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function 1998 10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>;2-b AcademicArticle Automated docking and the search for HIV protease inhibitors 1998 10.1080/10629369808039144 9522477 AcademicArticle Interactive modeling of supramolecular assemblies 1998 10.1016/s1093-3263(98)00016-3 10434250 AcademicArticle Defining GC-specificity in the minor groove: Side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G 1997 10.1016/s0969-2126(97)00255-4 9309219 AcademicArticle The art of molecular graphics - Irving Geis: Dean of molecular illustration 1997 10.1016/s1093-3263(97)82817-3 AcademicArticle Progress in the design of DNA sequence-specific lexitropsins 1997 10.1002/(sici)1097-0282(1997)44:4<323::aid-bip2>;2-0 9782774 AcademicArticle Estimation of the DNA sequence discriminatory ability of hairpin-linked lexitropsins 1997 10.1073/pnas.94.11.5634 9159124 AcademicArticle Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method 1997 10.1023/a:1007985019866 9491346 AcademicArticle MPD and DNA bending in crystals and in solution 1996 10.1006/jmbi.1996.0071 8609604 AcademicArticle Automated docking of flexible ligands: applications of AutoDock 1996 10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>;2-6 8723313 AcademicArticle Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 1996 10.1007/bf00124499 8877701 AcademicArticle 1994 Molecular Graphics Art Show and Video Show 1995 10.1016/0263-7855(95)00036-6 8527415 AcademicArticle Refinement of netropsin bound to DNA - bias and feedback in electron-density map interpretation 1995 10.1021/bi00015a009 7711020 AcademicArticle Crystal-structure of C-T-C-T-C-G-A-G-A-G - implications for the structure of the Holliday junction 1995 10.1021/bi00003a037 7827018 AcademicArticle Design of B-DNA cross-linking and sequence-reading molecules 1995 10.1002/bip.360350513 7766821 AcademicArticle Structure of a dicationic monoimidazole lexitropsin bound to DNA 1995 10.1021/bi00051a013 8527438 AcademicArticle Crystal-structure of a covalent DNA drug adduct - anthramycin bound to C-C-A-A-C-G-T-T-G-G and a molecular explanation of specificity 1994 10.1021/bi00250a011 7947769 AcademicArticle ... The tyranny of the lattice 1994 10.1073/pnas.91.9.3579 8170950 AcademicArticle Molecular graphics art show 1994 AcademicArticle Bending and curvature calculations in B-DNA 1994 10.1093/nar/22.24.5497 7816643 AcademicArticle The crystal-structure of C-C-A-T-T-A-A-T-G-G - implications for bending of B-DNA at T-A steps 1994 10.1006/jmbi.1994.1352 8196049 AcademicArticle Soluble proteins: size, shape and function 1993 10.1016/0968-0004(93)90153-e 8480362 AcademicArticle Crystal-structure of CATGGCCATG and its implications for A-tract bending models 1993 10.1073/pnas.90.7.2930 8464909 AcademicArticle Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA 1993 10.1021/bi00085a025 8364037 AcademicArticle Automated docking in crystallography: analysis of the substrates of aconitase 1993 10.1002/prot.340170104 8234239 AcademicArticle Macromolecular graphics 1992 10.1016/0959-440X(92)90146-X AcademicArticle Molecular illustration in black and white 1992 10.1016/0263-7855(92)80075-o 1476997 AcademicArticle A look inside the living cell 1992 AcademicArticle Visualizing biological molecules 1992 1411463 AcademicArticle Visualization Blackboard: a functional view of proteins 1991 AcademicArticle Molecular illustration 1991 AcademicArticle Inside a living cell 1991 10.1016/0968-0004(91)90083-8 1891800 AcademicArticle A functional view of proteins 1991 10.1109/MCG.1991.10002 AcademicArticle Automated docking of substrates to proteins by simulated annealing 1990 10.1002/prot.340080302 2281083 AcademicArticle The structure of DAPI bound to DNA 1989 2627296 AcademicArticle Rendering volumetric data in molecular systems 1989 10.1016/0263-7855(89)80055-4 AcademicArticle RMS: Programs for generating raster molecule surfaces 1988 10.1016/0263-7855(88)80058-4 AcademicArticle Structure of an alternating-B DNA helix and its relationship to A-tract DNA 1988 10.1073/pnas.85.17.6332 3413099 AcademicArticle The effect of crystal packing on oligonucleotide double helix structure 1987 2482757 AcademicArticle Isohelical analysis of DNA groove-binding drugs 1986 10.1021/jm00155a023 2422377 AcademicArticle The molecular-origin of DNA drug specificity in netropsin and distamycin 1985 10.1073/pnas.82.5.1376 2983343 AcademicArticle Binding of an antitumor drug to DNA netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G 1985 10.1016/0022-2836(85)90171-8 2991536