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mdimmics library [130 articles]

Neue Artikel in mdimmics ordered by to_read.
  • Single-Molecule, Motion-Based DNA Sequencing Using RNA Polymerase
    Science, Vol. 313, No. 5788. (11 August 2006), 801.
    by William J Greenleaf, Steven M Block
    posted to nanodetection protein-dna-interaction by mdimmic on 2006-11-09 19:28:36 as ***** along with 3 people and 2 groups dayjm dchughes eyliu G4ID Genetics-of-Gambling
  • Closed and open conformations of the lid domain induce different patterns of human pancreatic lipase antigenicity and immunogenicity
    Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1753, No. 2. (1 December 2005), pp. 247-256.
    by Hubert Halimi, Josiane De Caro, Frederic Carriere, Alain De Caro
    posted to epitope-design by mdimmic on 2005-11-23 17:45:54 as *****
  • NdPASA: a pairwise sequence alignment server for distantly related proteins.
    Bioinformatics, Vol. 21, No. 19. (1 October 2005), pp. 3803-3805.
    by W Li, J Wang, JA Feng
    posted to homolog-detection sequence-alignment by mdimmic on 2005-10-28 00:43:44 as *****
  • Mimotopes: realization of an unlikely concept
    Journal of Molecular Recognition, Vol. 13, No. 6. (15 November 2000), pp. 352-359.
    by RH Meloen, WC Puijk, JW Slootstra
    posted to epitope-design review by mdimmic on 2005-10-15 00:08:57 as *****
  • Structure-immunogenicity relationships of therapeutic proteins.
    Pharm Res, Vol. 21, No. 6. (June 2004), pp. 897-903.
    by S Hermeling, DJ Crommelin, H Schellekens, W Jiskoot
    posted to epitope-design review by mdimmic on 2005-08-25 21:09:06 as *****
  • Reverse vaccinology.
    Curr Opin Microbiol, Vol. 3, No. 5. (October 2000), pp. 445-450.
    by R Rappuoli
    posted to epitope-design by mdimmic on 2005-08-25 20:39:12 as *****
  • notes Evidence for a role of the N terminus and leucine-rich repeat region of the Mi gene product in regulation of localized cell death.
    Plant Cell, Vol. 12, No. 8. (August 2000), pp. 1319-1329.
    by CF Hwang, AV Bhakta, GM Truesdell, WM Pudlo, VM Williamson
    posted to plant-resistance receptor-activation transgenics by mdimmic on 2005-08-11 17:45:49 as ***** along with 1 person kikubh
  • Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly.
    Curr Opin Chem Biol, Vol. 8, No. 4. (August 2004), pp. 399-406.
    by DA Erlanson, SK Hansen
    posted to drug-development review by mdimmic on 2005-07-21 22:46:17 as ***** along with 2 people and 3 groups sangeetha kengg Bioinformatics insilicodrug Plantandetc
  • Small-molecule inhibitors of protein-protein interactions: progressing towards the dream.
    Nat Rev Drug Discov, Vol. 3, No. 4. (April 2004), pp. 301-317.
    by MR Arkin, JA Wells
    posted to drug-development protein-interaction review by mdimmic on 2005-07-21 22:40:49 as ***** along with 6 people dgruiz lna bicko dailybiomed Dualsystems ramensky
  • Creating small-molecule-dependent switches to modulate biological functions.
    Chem Biol, Vol. 12, No. 2. (February 2005), pp. 151-161.
    by AR Buskirk, DR Liu
    posted to protein-engineering receptor-activation review by mdimmic on 2005-07-08 03:23:54 as ***** along with 4 people rklancer lna monod grahamc
  • Directed evolution of specific receptor-ligand pairs for use in the creation of gene switches.
    Proc Natl Acad Sci U S A, Vol. 102, No. 16. (19 April 2005), pp. 5691-5696.
    by K Chockalingam, Z Chen, JA Katzenellenbogen, H Zhao
    posted to nanodetection protein-engineering receptor-activation by mdimmic on 2005-07-08 03:22:21 as *****
  • Ligand-receptor engineering and its application towards the complementation of genetic disease and target identification.
    Curr Top Med Chem, Vol. 5, No. 4. (2005), pp. 413-420.
    by JT Koh, JB Biggins
    posted to protein-engineering receptor-activation review by mdimmic on 2005-07-08 03:13:14 as *****
  • Creation and discovery of ligand-receptor pairs for transcriptional control with small molecules.
    Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14707-14712.
    by LJ Schwimmer, P Rohatgi, B Azizi, KL Seley, DF Doyle
    posted to protein-engineering receptor-activation by mdimmic on 2005-07-08 03:10:47 as *****
  • Engineering orthogonal ligand-receptor pairs from "near drugs".
    J Am Chem Soc, Vol. 123, No. 46. (21 November 2001), pp. 11367-11371.
    by DF Doyle, DA Braasch, LK Jackson, HE Weiss, MF Boehm, DJ Mangelsdorf, DR Corey
    posted to protein-engineering receptor-activation by mdimmic on 2005-07-08 03:10:06 as *****
  • OrthoMCL: identification of ortholog groups for eukaryotic genomes.
    Genome Res, Vol. 13, No. 9. (September 2003), pp. 2178-2189.
    by L Li, CJ Stoeckert, DS Roos
    posted to homolog-detection by mdimmic on 2005-07-07 21:10:52 as ***** along with 10 people and 2 groups dullhunk natstreet druvus tharris operon indigoviolet AaronDarling bluto maximilianh ninch C. elegans / WormBase EisenLab
  • Inparanoid: a comprehensive database of eukaryotic orthologs.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by KP O'Brien, M Remm, EL Sonnhammer
    posted to homolog-detection by mdimmic on 2005-07-01 00:04:33 as ***** along with 8 people and 2 groups tharris tmmurali dragonrez indigoviolet tny bluto incovoma jandot C. elegans / WormBase EisenLab
  • Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity
    Journal of Molecular Biology, Vol. 350, No. 3. (15 July 2005), pp. 402-415.
    by Michele Raviscioni, Peili Gu, Minawar Sattar, Austin J Cooney, Olivier Lichtarge
    posted to coevolution compensatory-changes protein-dna-interaction by mdimmic on 2005-06-23 17:01:05 as ***** along with 4 people kaarsinogen chrn lulab cjeans
  • Analytical methods for studying the evolution of paralogs using duplicate gene datasets.
    Methods Enzymol, Vol. 395 (2005), pp. 724-745.
    by S Mathews
    posted to functional-shift protein-evolution review by mdimmic on 2005-06-13 16:25:27 as *****
  • An integrated approach for inference and mechanistic modeling for advancing drug development
    FEBS Letters, Vol. 579, No. 8. (21 March 2005), pp. 1878-1883.
    by Sergej V Aksenov, Bruce Church, Anjali Dhiman, Anna Georgieva, Ramesh Sarangapani, Gabriel Helmlinger, Iya G Khalil
    posted to drug-development protein-interaction by mdimmic on 2005-06-02 22:05:37 as ***** along with 2 people snuppepuppan Borelli
  • Use of Logic Relationships to Decipher Protein Network Organization
    Science, Vol. 306, No. 5705. (24 December 2004), pp. 2246-2249.
    by Peter M Bowers, Shawn J Cokus, David Eisenberg, Todd O Yeates
    posted to protein-interaction by mdimmic on 2005-06-02 21:41:59 as ***** along with 3 people and 1 group lfriedl opheliav wnpx kdl
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
    Proc Natl Acad Sci U S A, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777.
    by B Ma, T Elkayam, H Wolfson, R Nussinov
    posted to coevolution protein-interaction by mdimmic on 2005-03-24 22:36:04 as ***** along with 8 people and 2 groups barry bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics Bioinformatics
  • Comparison of the protein-protein interfaces in the p53-DNA crystal structures: Towards elucidation of the biological interface.
    Proc Natl Acad Sci U S A, Vol. 102, No. 11. (15 March 2005), pp. 3988-3993.
    by B Ma, Y Pan, K Gunasekaran, RB Venkataraghavan, AJ Levine, R Nussinov
    posted to coevolution protein-interaction by mdimmic on 2005-03-24 22:35:51 as *****
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294.
    by O Keskin, B Ma, R Nussinov
    posted to coevolution protein-interaction by mdimmic on 2005-03-24 22:35:40 as ***** along with 8 people and 2 groups ana barry baaden okarsligil bicko j3xucite bilab xz structural_bioinformatics Bioinformatics
  • Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.
    Genome Res, Vol. 13, No. 6A. (June 2003), pp. 1146-1154.
    by L Lu, AK Arakaki, H Lu, J Skolnick
    posted to coevolution protein-interaction by mdimmic on 2005-03-24 22:33:48 as ***** along with 5 people and 1 group bicko lfriedl chad_davis ruvido cjeans kdl
  • Development of unified statistical potentials describing protein-protein interactions.
    Biophys J, Vol. 84, No. 3. (March 2003), pp. 1895-1901.
    by H Lu, L Lu, J Skolnick
    posted to coevolution protein-interaction by mdimmic on 2005-03-24 22:33:29 as ***** along with 7 people bicko chad_davis cjeans selrac iris_2001 wilbur kgutwin
  • Biosensors based on binding-modulated donor-acceptor distances
    Trends in Biotechnology, Vol. 23, No. 4. (April 2005), pp. 186-192.
    by Chunhai Fan, Kevin W Plaxco, Alan J Heeger
    posted to nanodetection by mdimmic on 2005-03-21 21:28:10 as *****
  • Fast Adaptive Coevolution of Nuclear and Mitochondrial Subunits of ATP Synthetase in Orangutan.
    Mol Biol Evol, Vol. 22, No. 3. (March 2005), pp. 716-724.
    by Maria Pilar P Bayona-Bafaluy, Stefan Müller, Carlos T T Moraes
    posted to coevolution protein-interaction by mdimmic on 2005-02-23 21:38:48 as *****
  • iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    Bioinformatics, Vol. 21, No. 3. (01 February 2005), 410.
    by Robert D Finn, Mhairi Marshall, Alex Bateman
    posted to coevolution protein-interaction by mdimmic on 2005-02-08 19:09:25 as ***** along with 6 people and 2 groups barry chad_davis choonpeng massivemayhem antonkratz kintoki structural_bioinformatics Bioinformatics
  • Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
    BMC Bioinformatics, Vol. 8 (25 August 2007), 310.
    by Luis A Diago, Persy Morell, Longendri Aguilera, Ernesto Moreno
    posted to ligand-docking by mdimmic on 2007-09-17 23:14:05 as **** along with 1 person massivemayhem
  • Recent Evolutions of Multiple Sequence Alignment Algorithms
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e123.
    by Cédric Notredame
    posted to review sequence-alignment by mdimmic on 2007-09-17 22:59:02 as **** along with 9 people and 2 groups rvosa timflutre stajich zwang cabbagezs groepl yoanjacquemin marti smbe2008 Bioinformatics FAB-lab
  • Enhanced immunogenicity of a conformational epitope of human T-lymphotropic virus type 1 using a novel chimeric peptide
    Vaccine, Vol. 19, No. 9-10. (8 December 2000), pp. 1068-1081.
    by Melanie Frangione-Beebe, Bjorn Albrecht, Naveen Dakappagari, Travis R Rose, Charles L Brooks, Steven P Schwendeman, Michael D Lairmore, Pravin T Kaumaya
    posted to epitope-design by mdimmic on 2006-05-22 21:12:18 as ****
  • Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences.
    Mol Biol Evol (21 September 2005)
    by Beth Shapiro, Andrew Rambaut, Alexei J J Drummond
    posted to phylogenetic-methods protein-evolution by mdimmic on 2005-11-23 16:33:05 as ****
  • Analysis of accessible surface of residues in proteins.
    Protein Sci, Vol. 12, No. 7. (July 2003), pp. 1406-1417.
    by L Lins, A Thomas, R Brasseur
    posted to epitope-design protein-interaction by mdimmic on 2005-10-13 23:15:18 as **** along with 1 person ashaytan
  • Multiple sequence alignments
    Current Opinion in Structural Biology, Vol. 15, No. 3. (June 2005), pp. 261-266.
    by Iain M Wallace, Gordon Blackshields, Desmond G Higgins
    posted to review sequence-alignment by mdimmic on 2005-09-30 22:18:25 as **** along with 2 people bpb nklee
  • Programmed cell death in the root cortex of soybean root necrosis mutants.
    Plant J, Vol. 11, No. 4. (April 1997), pp. 729-745.
    by RM Kosslak, MA Chamberlin, RG Palmer, BA Bowen
    posted to plant-resistance transgenics by mdimmic on 2005-09-27 23:05:09 as ****
  • Predictive estimation of protein linear epitopes by using the program PEOPLE.
    Vaccine, Vol. 18, No. 3-4. (September 1999), pp. 311-314.
    by AJ Alix
    posted to epitope-design by mdimmic on 2005-08-26 01:17:55 as **** along with 1 person leelarcombe
  • The role of structure in antibody cross-reactivity between peptides and folded proteins.
    J Mol Biol, Vol. 281, No. 1. (7 August 1998), pp. 183-201.
    by L Craig, PC Sanschagrin, A Rozek, S Lackie, LA Kuhn, JK Scott
    posted to epitope-design by mdimmic on 2005-08-25 22:33:00 as **** along with 1 person leelarcombe
  • Candidate epitope identification using peptide property models: application to cancer immunotherapy.
    Methods, Vol. 34, No. 4. (December 2004), pp. 460-467.
    by MH Sung, R Simon
    posted to epitope-design review by mdimmic on 2005-08-25 21:14:44 as **** along with 1 person and 1 group okarsligil Bioinformatics
  • Searching for new allosteric sites in enzymes.
    Curr Opin Struct Biol, Vol. 14, No. 6. (December 2004), pp. 706-715.
    by JA Hardy, JA Wells
    posted to drug-development review by mdimmic on 2005-07-21 22:58:13 as **** along with 4 people apaydin lna aqeel higueruelo
  • Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor.
    Proc Natl Acad Sci U S A, Vol. 102, No. 8. (22 February 2005), pp. 2719-2724.
    by E Buck, JA Wells
    posted to drug-development target-discovery-expt by mdimmic on 2005-07-21 22:49:54 as ****
  • Making protein interactions druggable: targeting PDZ domains.
    Nat Rev Drug Discov, Vol. 3, No. 12. (December 2004), pp. 1047-1056.
    by KK Dev
    posted to drug-development protein-interaction review by mdimmic on 2005-07-21 22:38:12 as **** along with 1 person jyuh
  • FunShift: a database of function shift analysis on protein subfamilies.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by S Abhiman, EL Sonnhammer
    posted to functional-shift by mdimmic on 2005-06-30 23:58:21 as ****
  • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
    Bioinformatics, Vol. 18, No. 1. (January 2002), pp. 92-99.
    by CE Storm, EL Sonnhammer
    posted to homolog-detection by mdimmic on 2005-06-30 23:39:48 as **** along with 5 people and 1 group operon rvosa dlr indigoviolet ninch EisenLab
  • Prediction of orthologous relationship by functionally important sites.
    Comput Methods Programs Biomed, Vol. 78, No. 3. (June 2005), pp. 209-222.
    by HC Chiu, CA Chang, YJ Hu
    posted to homolog-detection by mdimmic on 2005-06-30 23:35:20 as ****
  • Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.
    Bioinformatics, Vol. 21, No. 6. (March 2005), pp. 703-710.
    by XH Zheng, F Lu, ZY Wang, F Zhong, J Hoover, R Mural
    posted to homolog-detection by mdimmic on 2005-06-30 23:29:58 as ****
  • Gene duplication, the evolution of novel gene functions, and detecting functional divergence of duplicates in silico.
    Appl Bioinformatics, Vol. 2, No. 2. (2003), pp. 91-101.
    by J Raes, Y Van de Peer
    posted to functional-shift protein-evolution by mdimmic on 2005-06-24 19:39:38 as **** along with 2 people imouthesmp Schmidtc
  • On the molecular discrimination between adenine and guanine by proteins.
    Nucleic Acids Res, Vol. 29, No. 21. (1 November 2001), pp. 4294-4309.
    by I Nobeli, RA Laskowski, WS Valdar, JM Thornton
    posted to nanodetection protein-dna-interaction by mdimmic on 2005-03-25 01:11:14 as ****
  • Prediction of Function Divergence in Protein Families Using the Substitution Rate Variation Parameter Alpha
    Molecular Biology and Evolution, Vol. 23, No. 7. (1 July 2006), pp. 1406-1413.
    by Abhiman, Saraswathi, Daub, O Carsten, Sonnhammer, LL Erik
    posted to functional-shift by mdimmic on 2006-06-13 17:15:24 as ***
  • Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA.
    J Mol Biol, Vol. 350, No. 2. (8 July 2005), pp. 290-299.
    by S Koide, X Yang, X Huang, JJ Dunn, BJ Luft
    posted to epitope-design by mdimmic on 2006-05-22 21:39:14 as ***
  • Synthesis, refolding and protective immune responses of a potential antigen for human Respiratory Syncytial Virus vaccine.
    J Pept Res, Vol. 62, No. 1. (July 2003), pp. 27-36.
    by C Klinguer-Hamour, MC Bussat, H Plotnicky, D Velin, N Corvaïa, T Nguyen, A Beck
    posted to epitope-design by mdimmic on 2006-05-19 23:54:46 as ***
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