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Tag ligand [121 articles]

Recent papers classified by the tag ligand.
  • Information Theory-Based Scoring Function for the Structure-Based Prediction of Protein−Ligand Binding Affinity
    J. Chem. Inf. Model. (4 September 2008)
    by Mahesh Kulharia, Roger S Goody, Richard M Jackson
    posted to scoring protein pair ligand function database contact binding atom affinity by zimbo1 on 2008-09-08 14:16:28 as **
  • notes Hierarchical docking of databases of multiple ligand conformations.
    Curr Top Med Chem, Vol. 5, No. 8. (2005), pp. 739-749.
    by DM Lorber, BK Shoichet
    posted to flex ligand by yongzhao on 2005-09-16 06:23:40 as ** along with 1 person and 1 group blackbart TSRI_MGL
  • The membrane-proximal scavenger receptor cysteine-rich domain of CD6 contains the activated leukocyte cell adhesion molecule binding site.
    J Biol Chem, Vol. 270, No. 31. (4 August 1995), pp. 18187-18190.
    by GS Whitney, GC Starling, MA Bowen, B Modrell, AW Siadak, A Aruffo
    posted to alcam cd6 ligand by swennemann on 2006-03-24 08:57:05 as read
  • Identification and characterization of a 100-kD ligand for CD6 on human thymic epithelial cells.
    J Exp Med, Vol. 181, No. 4. (1 April 1995), pp. 1563-1568.
    by DD Patel, SF Wee, LP Whichard, MA Bowen, JM Pesando, A Aruffo, BF Haynes
    posted to cd6 epithel ligand thymic by swennemann on 2006-03-24 08:48:11 as read
  • New and Original pKa Prediction Method Using Grid Molecular Interaction Fields
    J. Chem. Inf. Model. (2 October 2007)
    by F Milletti, L Storchi, G Sforna, G Cruciani
    posted to ligand pka prediction by sim82 on 2008-03-10 09:22:13 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Untitled
    posted to binding by computational contribution energy evaluation free ligand methods molecules of protein the to water by sangeetha on 2006-05-01 08:59:29 as ** along with 2 groups Bioinformatics insilicodrug
  • 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 discovery ligand by sangeetha on 2006-01-25 09:21:10 as ** along with 2 people and 3 groups mdimmic kengg Bioinformatics insilicodrug Plantandetc
  • Ligand Stabilization of the β2 Adrenergic Receptor: Effect of DTT on Receptor Conformation Monitored by Circular Dichroism and Fluorescence Spectroscopy
    Biochemistry, Vol. 35, No. 46. (19 November 1996), pp. 14445-14451.
    by S Lin, U Gether, BK Kobilka
    posted to gpcr imp ligand by rph on 2008-05-27 17:25:29 as ** along with 1 person jddowney
  • (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
    Chemphyschem : a European journal of chemical physics and physical chemistry, Vol. 9, No. 7. (16 May 2008), pp. 983-988.
    by R Baron, JA McCammon
    posted to binding dynamics entropy flexibility ligand method molecular protein quasi-harmonic receptor by rbaron on 2008-08-05 01:53:58 as read along with 1 person higueruelo
  • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
    J Comput Aided Mol Des (15 January 2008)
    by Rommie E Amaro, Riccardo Baron, J A McCammon
    posted to screening receptor molecular ligand flexibility dynamics drug docking binding by rbaron on 2008-09-11 18:37:21 as read along with 4 people and 1 group jmccammon higueruelo kazemi LamBras McCammon
  • Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids
    Molecular Simulation, Vol. 34, No. 4. (2008), pp. 349-364.
    by MB Tessier, ML Demarco, AB Yongye, RJ Woods
    posted to amber force_field ligand by RamuAnandakrishnan on 2008-06-17 18:14:43 as **
  • A molecular mechanics force field for lignin
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Loukas Petridis, Jeremy C Smith
    posted to ligand md by RamuAnandakrishnan on 2008-08-03 15:37:26 as **
  • Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2347-2355.
    by Richard J Morris, Rafael J Najmanovich, Abdullah Kahraman, Janet M Thornton
    posted to ligand qualifier by RamuAnandakrishnan on 2007-10-15 23:52:48 as ** along with 1 person kallberg
  • DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Ying Gao, Dominique Douguet, Andrey Tovchigrechko, Ilya A Vakser
    posted to ligand by RamuAnandakrishnan on 2007-10-25 01:14:21 as *** along with 4 people marti bicko chad_davis timg
  • Computational prediction of the binding site of proteinase 3 to the plasma membrane
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis, Nathalie Reuter
    posted to binding_site electrostatics implicit_solvent ligand md by RamuAnandakrishnan on 2008-01-07 14:43:43 as **
  • Automated prediction of ligand-binding sites in proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Rodney Harris, Arthur J Olson, David S Goodsell
    posted to binding_site ligand qualifier by RamuAnandakrishnan on 2007-10-25 01:05:21 as ** along with 2 people tjimenez carlescorbi
  • Electrostatic properties of protein-protein complexes.
    Biophys J, Vol. 91, No. 5. (September 2006), pp. 1724-1736.
    by PJ Kundrotas, E Alexov
    posted to electrostatics ligand pka by RamuAnandakrishnan on 2007-10-15 15:49:47 as ** along with 1 person choonpeng
  • Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Weihua Li, Yun Tang, Hong Liu, Jiagao Cheng, Weiliang Zhu, Hualiang Jiang
    posted to homology ligand md by RamuAnandakrishnan on 2007-11-15 19:16:26 as **
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to electrostatics ligand pka by RamuAnandakrishnan on 2007-10-12 13:42:54 as **** along with 5 people and 3 groups csrocha bicko chad_davis sobolevnrm barry baker-group structural_bioinformatics McCammon
  • Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Mary H Cheng, Rob D Coalson, Michael Cascio
    posted to binding_site ligand md by RamuAnandakrishnan on 2007-11-15 19:08:17 as ** along with 1 person LamBras
  • Computational modeling reveals molecular details of epidermal growth factor binding.
    BMC Cell Biol, Vol. 6 (2005)
    by K Mayawala, DG Vlachos, JS Edwards
    posted to ligand simulation structure by pjasper on 2007-04-19 18:45:46 as **
  • EGFR signaling leads to downregulation of PTP-LAR via TACE-mediated proteolytic processing.
    Cell Signal, Vol. 18, No. 9. (September 2006), pp. 1515-1527.
    by JE Ruhe, S Streit, S Hart, A Ullrich
    posted to ligand processing by pjasper on 2007-04-25 18:40:10 as **
  • Transient Suppression of Ligand-mediated Activation of Epidermal Growth Factor Receptor by Tumor Necrosis Factor-alpha through the TAK1-p38 Signaling Pathway.
    J Biol Chem, Vol. 282, No. 17. (27 April 2007), pp. 12698-12706.
    by P Singhirunnusorn, Y Ueno, M Matsuo, S Suzuki, I Saiki, H Sakurai
    posted to egfr ligand p38 tnfa by pjasper on 2007-05-08 18:35:10 as ** along with 1 person jyuh
  • Alteration of the serum levels of the epidermal growth factor receptor and its ligands in patients with non-small cell lung cancer and head and neck carcinoma
    British Journal of Cancer, Vol. aop, No. current. (24 April 2007)
    by Y Lemos-Gonzalez, FJ Rodriguez-Berrocal, OJ Cordero, C Gomez, Paez
    posted to egf ligand nsclc by pjasper on 2007-05-08 20:59:01 as **
  • Ectodomain shedding of the EGF-receptor ligand epigen is mediated by ADAM17.
    FEBS Lett, Vol. 581, No. 1. (9 January 2007), pp. 41-44.
    by U Sahin, CP Blobel
    posted to adam epigen ligand by pjasper on 2007-04-26 17:37:39 as **
  • ADAM-mediated ectodomain shedding of HB-EGF in receptor cross-talk.
    Biochim Biophys Acta, Vol. 1751, No. 1. (1 August 2005), pp. 110-117.
    by S Higashiyama, D Nanba
    posted to hbegf ligand review by pjasper on 2007-04-18 20:36:49 as **
  • Targeting TACE-dependent EGFR ligand shedding in breast cancer.
    J Clin Invest, Vol. 117, No. 2. (February 2007), pp. 337-345.
    by PA Kenny, MJ Bissell
    posted to breast egfr ligand tace by pjasper on 2007-05-08 18:17:31 as **
  • Current methods for site-directed structure generation
    Journal of Computer-Aided Molecular Design, Vol. 8, No. 4. (1994), pp. 467-475.
    by Richard A Lewis, Andrew R Leach
    posted to automated growth ligand by peprovy on 2007-10-11 15:17:49 as read
  • A validation study on the practical use of automated de novo design
    Journal of Computer-Aided Molecular Design, Vol. 16, No. 7. (1 July 2002), pp. 459-478.
    by Martin Stahl, Nikolay P Todorov, Tim James, Harald Mauser, Hans-Joachim Boehm, Philip M Dean
    posted to automated de design generation ligand novo skelgen by peprovy on 2007-10-11 15:12:52 as read
  • A Quantitative Model of Thermal Stabilization and Destabilization of Proteins by Ligands
    Biophys. J., Vol. 95, No. 7. (1 October 2008), pp. 3222-3231.
    by Piotras Cimmperman, Lina Baranauskiene, Simona Jachimoviciute, Jelena Jachno, Jolanta Torresan, Vilma Michailoviene, Jurgita Matuliene, Jolanta Sereikaite, Vladas Bumelis, Daumantas Matulis
    posted to thermal stabiliztion ligand cimmp08pdf by paulschlesinger on 2008-09-24 01:03:38 as **
  • Determination of the Two-Dimensional Interaction Rate Constants of a Cytokine Receptor Complex
    Biophys. J., Vol. 90, No. 9. (1 May 2006), pp. 3345-3355.
    by Martynas Gavutis, Eva Jaks, Peter Lamken, Jacob Piehler
    posted to receptor oligomerization membrane ligand interaction gavut06pdf by paulschlesinger on 2008-09-10 19:08:16 as **
  • Blockade of the Fas/Fas ligand interaction suppresses hepatocyte apoptosis in ischemia-reperfusion rat liver
    Apoptosis
    by Hiroo Nakajima, Naruhiko Mizuta, Ikuya Fujiwara, Koichi Sakaguchi, Hiromitsu Ogata, Junji Magae, Hideo Yagita, Takehiko Koji
    posted to apoptosis fas ligand by paulschlesinger on 2008-06-20 01:00:17 as **
  • Protein-Ligand Complexes: Computation of the Relative Free Energy of Different Scaffolds and Binding Modes
    J. Chem. Theory Comput. (4 August 2007)
    by J Michel, ML Verdonk, JW Essex
    posted to energy free ligand protein receptors by paulschlesinger on 2007-08-23 00:18:54 as ** along with 1 person daevans
  • De novo ligand design to an ensemble of protein structures.
    Proteins (22 March 2006)
    by N P P Todorov, C L L Buenemann, I L L Alberts
    posted to ligand design by npt11tpn on 2007-01-10 20:14:58 as ** along with 1 person kentsis
  • Receptor flexibility in de novo ligand design and docking.
    J Med Chem, Vol. 48, No. 21. (20 October 2005), pp. 6585-6596.
    by IL Alberts, NP Todorov, PM Dean
    posted to ligand design by npt11tpn on 2007-01-09 23:14:39 as read along with 5 people and 1 group BragilMassoud dgruiz apaydin yongzhao kazemi TSRI_MGL
  • Ligand selectivity and competition between enzymes in silico.
    Nat Biotechnol, Vol. 22, No. 8. (August 2004), pp. 1039-1045.
    by A Macchiarulo, I Nobeli, JM Thornton
    posted to ligand enzyme by noby on 2007-01-29 04:51:12 as ** along with 4 people BragilMassoud kuhn bicko tny
  • The role of selectins in inflammation and disease.
    Trends Mol Med, Vol. 9, No. 6. (June 2003), pp. 263-268.
    by K Ley
    posted to 1 glycoprotein ligand p-selectin by nm on 2006-12-21 07:57:13 as **
  • Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.
    Proteins (1 May 2008)
    by Mizuki Morita, Shugo Nakamura, Kentaro Shimizu
    posted to apo energy-based ligand prediction protein strcuture by nickolay on 2008-07-14 20:02:25 as **
  • sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank.
    J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727.
    by E Kellenberger, P Muller, C Schalon, G Bret, N Foata, D Rognan
    posted to binding database drug ligand protein site by nickolay on 2008-08-27 15:49:30 as read along with 6 people and 1 group BragilMassoud caporaso schlauchi daevans ramensky sim82 biomedical-nlp
  • A simple and fuzzy method to align and compare druggable ligand-binding sites
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Claire Schalon, Jean-Sébastien Surgand, Esther Kellenberger, Didier Rognan
    posted to binding comparison fingerprint ligand protein similarity site by nickolay on 2008-08-27 14:14:35 as read along with 3 people tjimenez bicko willpitt
  • Protein-ligand interactions: exchange processes and determination of ligand conformation and protein-ligand contacts.
    Methods Enzymol, Vol. 239 (1994), pp. 657-700.
    by LY Lian, IL Barsukov, MJ Sutcliffe, KH Sze, GC Roberts
    posted to binding ligand protein-ligand structure-function by nickolay on 2006-08-18 18:53:54 as **** along with 1 person dgruiz
  • On the perception of molecules from 3D atomic coordinates.
    J Chem Inf Model, Vol. 45, No. 2. (r 2005), pp. 215-221.
    by P Labute
    posted to chemistry ligand method moe structure by nickolay on 2006-06-27 02:02:35 as read
  • Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy.
    J Am Chem Soc, Vol. 126, No. 43. (3 November 2004), pp. 13948-13953.
    by SG Zech, E Olejniczak, P Hajduk, J Mack, AE McDermott
    posted to ligand nmr shift ssnmr by netterpaladin on 2007-10-24 14:26:02 as ** along with 1 person viktor21614
  • Mapping protein-protein interaction by 13C'-detected heteronuclear NMR spectroscopy.
    J Biomol NMR, Vol. 36, No. 2. (October 2006), pp. 111-122.
    by I Bertini, IC Felli, L Gonnelli, R Pierattelli, Z Spyranti, GA Spyroulias
    posted to ligand nmr shift by netterpaladin on 2007-10-24 14:28:29 as ** along with 1 person viktor21614
  • Crystal Structure of the FK506 Binding Domain of Plasmodium falciparum FKBP35 in Complex with FK506
    Biochemistry (9 May 2008)
    by Masayo Kotaka, Hong Ye, Reema Alag, Guangan Hu, Zbynek Bozdech, Peter R Preiser, Ho S Yoon, Julien Lescar
    posted to crystallography fkbp ligand plasmodium structure complex by neils on 2008-05-09 06:57:49 as ** along with 1 person becarmson
  • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111.
    by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton
    posted to binding discrimination ligand protein similarity structure by neils on 2008-08-11 00:37:28 as ** along with 2 people reyez nickolay
  • Ligand binding affinity prediction by linear interaction energy methods
    Journal of Computer-Aided Molecular Design, Vol. 12, No. 1. (1 January 1998), pp. 27-35.
    by Tomas Hansson, John Marelius, Johan Åqvist
    posted to affinity binding bioinformatics lie ligand prediction by neils on 2008-04-15 02:18:54 as **
  • MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Nicolas Sauton, David Lagorce, Bruno Villoutreix, Maria Miteva
    posted to conformation docking screen software virtual ligand by neils on 2008-04-11 01:48:58 as ** along with 1 person biehl
  • Selectivity and affinity determinants for ligand binding to the aromatic amino acid hydroxylases.
    Current medicinal chemistry, Vol. 14, No. 4. (2007), pp. 455-467.
    by K Teigen, JA McKinney, J Haavik, A Martínez
    posted to binding hpah ligand structure by min013 on 2008-04-23 13:02:20 as **
  • Distance Dependent Scoring Function for Describing Protein-Ligand Intermolecular Interactions
    J. Chem. Inf. Model. (22 February 2008)
    by N Artemenko
    posted to interactions ligand protein scoring_functions by middledomain on 2008-02-22 14:42:52 as **
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