mijogiffin's library 129 articles Export

	ProFunc: a server for predicting protein function from 3D structure [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W89-93. by Roman A. Laskowski, James D. Watson, Janet M. Thornton posted to prediction modeling by mijogiffin on 2009-11-13 18:37:01 as along with 2 people gbart siebertm
	Investigating interactions between HIV-1 gp41 and inhibitors by molecular dynamics simulation and MM–PBSA/GBSA calculations [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 766, No. 2-3. (15 August 2006), pp. 77-82. by Jian J. Tan, Wei Z. Chen, Cun X. Wang posted to modeling md by mijogiffin on 2009-10-31 15:40:14 as along with 1 person and 1 group sobolevnrm baker-group
	Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. [My Copy] Journal of computer-aided molecular design, Vol. 19, No. 11. (November 2005), pp. 765-770. by Christophe Chipot, Xavier Rozanska, Surjit B. Dixit posted to modeling md by mijogiffin on 2009-10-31 15:38:49 as
	Biomolecular modeling: Goals, problems, perspectives. [My Copy] Angewandte Chemie (International ed. in English), Vol. 45, No. 25. (19 June 2006), pp. 4064-4092. by Wilfred F. van Gunsteren, Dirk Bakowies, Riccardo Baron, et al.Indira Chandrasekhar, Markus Christen, Xavier Daura, Peter Gee, Daan P. Geerke, Alice Glättli, Philippe H. Hünenberger, Mika A. Kastenholz, Chris Oostenbrink, Merijn Schenk, Daniel Trzesniak, Nico F. van der Vegt, Haibo B. Yu posted to modeling md by mijogiffin on 2009-10-31 15:38:20 as along with 2 people patricia LamBras
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted to mmpbsa md by mijogiffin on 2009-10-25 19:56:40 as along with 15 people and 3 groups flbarroso GermanErlenkamp onufriev arlam oteri jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	Free energy perturbation and molecular dynamics calculations of copper binding to azurin [My Copy] Journal of Computational Chemistry, Vol. 24, No. 6. (2003), pp. 779-785. by Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa posted to md by mijogiffin on 2009-10-25 19:49:27 as
	PyEvolve: a toolkit for statistical modelling of molecular evolution. [My Copy] BMC bioinformatics, Vol. 5, No. 1. (5 January 2004) by Andrew Butterfield, Vivek Vedagiri, Edward Lang, et al.Cath Lawrence, Matthew J. Wakefield, Alexander Isaev, Gavin A. Huttley posted to protein molecular modeling evolution by mijogiffin on 2009-10-05 01:34:00 as along with 1 person operon
	Protinfo PPC: A web server for atomic level prediction of protein complexes [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W519-525. by Weerayuth Kittichotirat, Michal Guerquin, Roger E. Bumgarner, Ram Samudrala posted to protein prediction modeling by mijogiffin on 2009-10-05 01:32:36 as along with 1 person guhjy
	Expression and function of erythropoietin receptors in tumors [My Copy] Cancer, Vol. 110, No. 3. (2007), pp. 477-488. by Angus M. Sinclair, Marque D. Todd, Kevin Forsythe, Susan J. Knox, Steve Elliott, C. Glenn Begley posted to epo amgen by mijogiffin on 2009-10-03 22:24:55 as
	Ligand efficiency: a useful metric for lead selection [My Copy] Drug Discovery Today, Vol. 9, No. 10. (15 May 2004), pp. 430-431. by A. Hopkins posted to ligand drug by mijogiffin on 2009-08-21 00:33:28 as along with 6 people ubcg08l bicko Yanno daevans higueruelo JALumley
	Evolutionary Profiles Derived from the QR Factorization of Multiple Structural Alignments Gives an Economy of Information [My Copy] Journal of Molecular Biology, Vol. 346, No. 3. (25 February 2005), pp. 875-894. by Patrick O'Donoghue, Zaida Luthey-Schulten posted to sequence qr alignment by mijogiffin on 2009-08-20 18:07:19 as
	Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy [My Copy] Biophysical Journal, Vol. 86, No. 1. (January 2004), pp. 67-74. by J. Swanson posted to mmpbsa md by mijogiffin on 2009-08-20 17:49:44 as
	Small-Molecule Inhibitors of HIV-1 Protease Dimerization Derived from Cross-Linked Interfacial Peptides [My Copy] Angewandte Chemie, Vol. 112, No. 15. (2000), pp. 2822-2825. by Michael d, Michael j, Young-Wan Ham, Xuimin Zhao, George Tora, Jean Chmielewski posted to dimer dissociative inhibitor protease by mijogiffin on 2009-07-22 18:26:00 as
	Flow: Statistics, visualization and informatics for flow cytometry [My Copy] Source Code for Biology and Medicine, Vol. 3, No. 1. (2008), 10. by Jacob Frelinger, Thomas Kepler, Cliburn Chan posted to facs by mijogiffin on 2009-07-22 06:00:51 as along with 3 people ajaymalik abhishek_tiwari guhjy
	A detergent-based assay for the detection of promiscuous inhibitors. [My Copy] Nature protocols, Vol. 1, No. 2. (2006), pp. 550-553. by B. Y. Feng, B. K. Shoichet posted to inhibition promiscuous by mijogiffin on 2009-07-18 00:13:36 as
	A Common Mechanism Underlying Promiscuous Inhibitors from Virtual and High-Throughput Screening [My Copy] Journal of Medicinal Chemistry, Vol. 45, No. 8. (1 April 2002), pp. 1712-1722. by Susan L. Mcgovern, Emilia Caselli, Nikolaus Grigorieff, Brian K. Shoichet posted to inhibition promiscuous by mijogiffin on 2009-07-18 00:12:44 as along with 1 person jerome_ucsf_slb
	Design of peptidomimetic inhibitors of aspartic protease of HIV-1 containing –PheΨPro– core and displaying favourable ADME-related properties [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 3. (October 2008), pp. 376-387. by V. Frecer, F. Berti, F. Benedetti, S. Miertus posted to drug hiv md protease by mijogiffin on 2009-07-07 22:34:19 as
	2D molecular graphics: a flattened world of chemistry and biology [My Copy] Brief Bioinform (30 March 2009), bbp013. by Peng Zhou, Zhicai Shang posted to interaction ligand protein by mijogiffin on 2009-07-07 00:57:16 as along with 5 people and 3 groups Zephyrus nanonan sobolevnrm dimka barry baker-group structural_bioinformatics McCammon
	Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. [My Copy] BMC bioinformatics, Vol. 8 (25 August 2007), 310. by L. A. Diago, P. Morell, L. Aguilera, E. Moreno posted to docking ligand by mijogiffin on 2009-06-30 03:06:47 as along with 3 people flbarroso mdimmic massivemayhem
	A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔTm [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 9. (1 May 2007), pp. 2240-2244. by Saher A. Shaikh, B. Jayaram posted to dna drug inhibitor prediction by mijogiffin on 2009-06-29 20:18:25 as
	Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization [My Copy] J. Chem. Inf. Model. (29 February 2008) by F. Dey, A. Caflisch posted to docking ligand by mijogiffin on 2009-05-20 17:17:03 as along with 2 people massivemayhem middledomain
	Automating document classification for the Immune Epitope Database [My Copy] BMC Bioinformatics, Vol. 8 (26 July 2007), 269. by Peng Wang, Alexander A. Morgan, Qing Zhang, Alessandro Sette, Bjoern Peters posted to database by mijogiffin on 2009-05-13 21:37:28 as along with 1 person etaylorg
	Phi value versus psi analysis. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 50. (14 December 2004), pp. 17327-17328. by A. R. Fersht posted to dihedral by mijogiffin on 2009-05-09 06:43:32 as along with 1 person gbart
	The linked phi psi chain plot for visual comparison of the backbone conformation of peptides and proteins. [My Copy] International journal of peptide and protein research, Vol. 45, No. 3. (March 1995), pp. 272-281. by R. D. McClain, B. W. Erickson posted to dihedral by mijogiffin on 2009-05-09 06:41:24 as
	Binding Kinetics of Darunavir to Human Immunodeficiency Virus Type 1 Protease Explain the Potent Antiviral Activity and High Genetic Barrier [My Copy] J. Virol., Vol. 81, No. 24. (15 December 2007), pp. 13845-13851. by Inge Dierynck, Mieke De Wit, Emmanuel Gustin, et al.Inge Keuleers, Johan Vandersmissen, Sabine Hallenberger, Kurt Hertogs posted to hiv inhibitor protease resistance spr by mijogiffin on 2009-05-01 22:41:31 as
	An analysis of conformational changes on proteinprotein association: implications for predictive docking [My Copy] Protein Eng., Vol. 12, No. 4. (1 April 1999), pp. 271-283. by Matthew J. Betts, Michael J. E. Sternberg posted to complex conformation docking prediction by mijogiffin on 2009-05-01 18:54:48 as along with 4 people boris_aguilar bicko ffranca chad_davis
	Quantitative Symmetry in Structure−Activity Correlations: The Near C2 Symmetry of Inhibitor/HIV Protease Complexes [My Copy] Journal of the American Chemical Society, Vol. 122, No. 18. (1 May 2000), pp. 4378-4384. by Shahar Keinan, David Avnir posted to hiv protease resistance symmetry by mijogiffin on 2009-04-10 19:34:05 as
	<I>In silico</I> analyses of substrate interactions with human serum paraoxonase 1 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 75, No. 2. (2009), pp. 486-498. by Xin Hu, Xiaohui Jiang, David E. Lenz, Douglas M. Cerasoli, Anders Wallqvist posted to ligand silico simulation by mijogiffin on 2009-03-24 16:10:00 as
	Relating sequence evolution of HIV1-protease to its underlying molecular mechanics [My Copy] Gene, Vol. 422, No. 1-2. (01 October 2008), pp. 30-36. by K. Hamacher posted to dynamics hiv protease simulation by mijogiffin on 2009-03-24 16:09:12 as along with 1 person aqeel
	Evolution of Human Immunodeficiency Virus Type 1 Protease Genotypes and Phenotypes In Vivo under Selective Pressure of the Protease Inhibitor Ritonavir [My Copy] J. Virol., Vol. 79, No. 16. (15 August 2005), pp. 10638-10649. by Wolfgang Resch, Neil Parkin, Terri Watkins, Janera Harris, Ronald Swanstrom posted to drug hiv resistance selection by mijogiffin on 2009-03-24 16:07:53 as
	Role of Minority Populations of Human Immunodeficiency Virus Type 1 in the Evolution of Viral Resistance to Protease Inhibitors [My Copy] J. Virol., Vol. 78, No. 8. (15 April 2004), pp. 4234-4247. by Charlotte Charpentier, Dominic E. Dwyer, Fabrizio Mammano, Denise Lecossier, Francois Clavel, Allan J. Hance posted to drug genotypic hiv resistance sequencing by mijogiffin on 2009-03-24 16:07:14 as
	Mutagenically Separated PCR Assay for Rapid Detection of M41L and K70R Zidovudine Resistance Mutations in CRF01_AE (Subtype E) Human Immunodeficiency Virus Type 1 [My Copy] Antimicrob. Agents Chemother., Vol. 46, No. 12. (1 December 2002), pp. 3861-3868. by Lay Myint, Koya Ariyoshi, Hua Yan, et al.Alexander J. Frater, Wattana Auwanit, Panita Pathipvanith, Kaneo Yamada, Masakazu Matsuda, Tomoko Chiba, Kazunori Fujita, Myra Mcclure, Jonathan N. Weber, Wataru Sugiura posted to cloning drug hiv resistance selection sequencing by mijogiffin on 2009-03-24 16:06:37 as
	Genotypic Testing for Human Immunodeficiency Virus Type 1 Drug Resistance [My Copy] Clin. Microbiol. Rev., Vol. 15, No. 2. (1 April 2002), pp. 247-277. by Robert W. Shafer posted to cloning genotypic hiv sequencing by mijogiffin on 2009-03-24 16:03:32 as
	Human immunodeficiency virus type 1 envelope gene structure and diversity in vivo and after cocultivation in vitro. [My Copy] J. Virol., Vol. 66, No. 2. (1 February 1992), pp. 875-885. by K. Kusumi, B. Conway, S. Cunningham, et al.A. Berson, C. Evans, A. K. Iversen, D. Colvin, M. V. Gallo, S. Coutre, E. G. Shpaer posted to cloning hiv pcr by mijogiffin on 2009-03-24 16:00:51 as
	Development of a yeast-based recombination cloning/system for the analysis of gene products from diverse human immunodeficiency virus type 1 isolates [My Copy] Journal of Virological Methods, Vol. 111, No. 2. (August 2003), pp. 111-120. by A. Marozsan posted to cloning hiv by mijogiffin on 2009-03-24 15:59:29 as
	Unique Small Molecule Entry Inhibitors of Hemorrhagic Fever Arenaviruses [My Copy] J. Biol. Chem., Vol. 283, No. 27. (4 July 2008), pp. 18734-18742. by Andrew M. Lee, Jillian M. Rojek, Christina F. Spiropoulou, et al.Anette T. Gundersen, Wei Jin, Alex Shaginian, Joanne York, Jack H. Nunberg, Dale L. Boger, Michael B. Oldstone, Stefan Kunz posted to no-tag by mijogiffin on 2009-03-24 15:41:19 as
	In silico and in vitro: identifying new drugs. [My Copy] Current drug targets, Vol. 9, No. 12. (December 2008), pp. 1054-1061. by I. Pauli, L. F. Timmers, R. A. Caceres, M. B. Soares, W. F. de Azevedo posted to drug in silico by mijogiffin on 2009-03-24 15:39:39 as
	Molecular mechanics methods for predicting protein-ligand binding. [My Copy] Physical chemistry chemical physics : PCCP, Vol. 8, No. 44. (28 November 2006), pp. 5166-5177. by Niu Huang, Chakrapani Kalyanaraman, Katarzyna Bernacki, Matthew P. Jacobson posted to dynamics ligand protein simulation by mijogiffin on 2009-03-24 15:39:03 as along with 4 people anuragsethi apaydin ucbcjbm superpyrin
	Immunity in natural SIV infections [My Copy] Journal of Internal Medicine, Vol. 265, No. 1., pp. 97-109. by G. Silvestri posted to hiv immunity siv by mijogiffin on 2009-03-24 15:31:44 as
	Metabolic soft spot identification and compound optimization in early discovery phases using MetaSite and LC-MS/MS validation. [My Copy] Journal of medicinal chemistry, Vol. 52, No. 2. (22 January 2009), pp. 329-335. by M. Trunzer, B. Faller, A. Zimmerlin posted to drug by mijogiffin on 2009-03-20 16:30:30 as along with 1 person nickolay
	Quantifying the Relationships among Drug Classes [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 4. (1 April 2008), pp. 755-765. by Jérôme Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet posted to discovery drug by mijogiffin on 2009-03-16 23:33:50 as along with 8 people and 1 group nickolay tjchen pauldobson dullhunk middledomain sobolevnrm ucbcjbm jerome_ucsf_slb baker-group
	Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation [My Copy] Journal of Computer-Aided Molecular Design by Xiaoqing Liu, Zhilong Xiu, Ce Hao posted to drug hiv protease resistance by mijogiffin on 2009-03-06 01:57:06 as
	Distance matrix-based approach to protein structure prediction. [My Copy] Journal of structural and functional genomics, Vol. 10, No. 1. (1 March 2009), pp. 67-81. by Andrzej Kloczkowski, Robert L. Jernigan, Zhijun Wu, et al.Guang Song, Lei Yang, Andrzej Kolinski, Piotr Pokarowski posted to hiv protease by mijogiffin on 2009-03-06 01:55:52 as
	Modulation of HIV-1 infectivity and cyclophilin A-dependence by Gag sequence and target cell type [My Copy] Retrovirology, Vol. 6 (02 March 2009), 21. by Saori, Allan J. Hance posted to cypa gag hiv by mijogiffin on 2009-03-06 01:48:13 as
	An in vitro and in vivo disconnect uncovered through high-throughput identification of botulinum neurotoxin A antagonists. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 8. (20 February 2007), pp. 2602-2607. by L. M. Eubanks, M. S. Hixon, W. Jin, et al.S. Hong, C. M. Clancy, W. H. Tepp, M. R. Baldwin, C. J. Malizio, M. C. Goodnough, J. T. Barbieri, E. A. Johnson, D. L. Boger, T. J. Dickerson, K. D. Janda posted to boger library by mijogiffin on 2009-02-27 02:11:20 as
	Discovery of Inhibitors of Aberrant Gene Transcription from Libraries of DNA Binding Molecules: Inhibition of LEF-1-Mediated Gene Transcription and Oncogenic Transformation. [My Copy] Journal of the American Chemical Society (13 February 2009) by James S S. Stover, Jin Shi, Wei Jin, Peter K K. Vogt, Dale L L. Boger posted to boger library by mijogiffin on 2009-02-27 02:05:53 as
	Dimer Disruption and Monomer Sequestration by Alkyl Tripeptides Are Successful Strategies for Inhibiting Wild-Type and Multidrug-Resistant Mutated HIV-1 Proteases† [My Copy] Biochemistry, Vol. 48, No. 2. (20 January 2009), pp. 379-387. by Ludovic Bannwarth, Thierry Rose, Laure Dufau, et al.Régis Vanderesse, Julien Dumond, Brigitte Jamart-Grégoire, Christophe Pannecouque, Erik De Clercq, Michèle Reboud-Ravaux posted to hiv inhibitor protease by mijogiffin on 2009-02-23 17:48:19 as
	Dynamics of "flap" structures in three HIV-1 protease/inhibitor complexes probed by total chemical synthesis and pulse-EPR spectroscopy. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 3. (28 January 2009), pp. 884-885. by V. Y. Torbeev, H. Raghuraman, K. Mandal, S. Senapati, E. Perozo, S. B. Kent posted to dynamics epr hiv protease by mijogiffin on 2009-02-11 21:49:46 as
	The Folding Free-Energy Surface of HIV-1 Protease: Insights into the Thermodynamic Basis for Resistance to Inhibitors. [My Copy] Journal of molecular biology (6 January 2009) by Amanda F F. Noel, Osman Bilsel, Agnita Kundu, Ying Wu, Jill A A. Zitzewitz, C Robert R. Matthews posted to no-tag by mijogiffin on 2009-02-07 21:02:22 as along with 1 person zwang
	Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation. [My Copy] The Journal of chemical physics, Vol. 130, No. 4. (28 January 2009) by R. B. Pandey, B. L. Farmer posted to dynamics molecular simulation by mijogiffin on 2009-02-07 18:58:00 as

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hiv	62
resistance	28
drug	23
protease	18
selection	14
cloning	12
protein	11
inhibitor	10
dynamics	8
pcr	8
sequencing	8
intein	7
md	7
molecular	7
mutation	7
susceptibility	7
ligand	6
modeling	6
nef	6
simulation	6
prediction	4
replication	4
docking	3
primer	3
purification	3
structure	3
topo	3
ucsd	3
boger	2
cell	2
dihedral	2
dna	2
fluorescence	2
genotypic	2
immunity	2
in	2
inhibition	2
library	2
mmpbsa	2
proliferation	2
promiscuous	2
quantitation	2
r8	2
recombination	2
review	2
rna	2
rt	2
silico	2
tl-3	2
transmission	2
vaccine	2
alignment	1
allosteric	1
amg531	1
amgen	1
aptamer	1
arrest	1
astrocyte	1
bioinformatics	1
clathrin	1
complex	1
conformation	1
crystallography	1
cypa	1
database	1
dimer	1
discovery	1
dissociative	1
disulfides	1
endnote	1
engineering	1
entry	1
epo	1
epr	1
evolution	1
facs	1
file-import-08-08-27	1
gag	1
genomics	1
hta	1
interaction	1
itp	1
kresge	1
lattice	1
leachate	1
lentivirus	1
lipopetide	1
luciferase	1
mechanics	1
nanotube	1
oligo	1
pdb	1
plastic	1
polarization	1
pratt	1
programming	1
qr	1
quantum	1
receptor	1
retrovirus	1
sequence	1
seronegative	1
siv	1
spr	1
symmetry	1
t-cell	1
vector	1
vitro	1

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