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Tag protein-ligand_interactions [28 articles]

Recent papers classified by the tag protein-ligand_interactions.
  • Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses
    Biophys. J., Vol. 93, No. 6. (15 September 2007), pp. 1895-1905.
    by Agnieszka Szarecka, Yan Xu, Pei Tang
    posted to protein-ligand_interactions quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-26 19:42:23 as read along with 1 person and 1 group aqeel baker-group
  • A quantum-chemical picture of hemoglobin affinity
    Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18451-18455.
    by RE Alcantara, C Xu, TG Spiro, V Guallar
    posted to protein-ligand_interactions quantum_mechanics by sobolevnrm on 2007-12-21 12:29:02 as read along with 1 group baker-group
  • Localizing frustration in native proteins and protein assemblies
    Proceedings of the National Academy of Sciences (5 December 2007), 0709915104.
    by Diego U Ferreiro, Joseph A Hegler, Elizabeth A Komives, Peter G Wolynes
    posted to bioinformatics molecular_simulation protein-ligand_interactions protein-protein_interactions structure by sobolevnrm on 2008-01-21 12:49:28 as read along with 2 people and 1 group cjeans cactus baker-group
  • Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing
    Journal of Molecular Biology, Vol. 377, No. 3. (28 March 2008), pp. 914-934.
    by Alan P Graves, Devleena M Shivakumar, Sarah E Boyce, Matthew P Jacobson, David A Case, Brian K Shoichet
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-03-25 11:10:59 as read along with 1 group baker-group
  • Quantifying the Relationships among Drug Classes
    J. Chem. Inf. Model. (13 March 2008)
    by J&#xe9 Hert, R&#xf4, Me, Michael J Keiser, John J Irwin, Tudor I Oprea, Brian K Shoichet
    posted to bioinformatics protein-ligand_interactions by sobolevnrm on 2008-04-24 11:24:27 as read along with 3 people and 1 group middledomain ucbcjbm jerome_ucsf_slb baker-group
  • Specificity in Molecular Design: A Physical Framework for Probing the Determinants of Binding Specificity and Promiscuity in a Biological Environment
    J. Phys. Chem. B, Vol. 111, No. 47. (29 November 2007), pp. 13419-13435.
    by ML Radhakrishnan, B Tidor
    posted to bioinformatics protein-ligand_interactions drugdesign by sobolevnrm on 2008-01-03 12:27:31 as read along with 1 group baker-group
  • Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Katrin Kupas, Alfred Ultsch, Gerhard Klebe
    posted to bioinformatics protein-ligand_interactions structure by sobolevnrm on 2007-12-27 12:17:15 as read along with 3 people and 1 group carlescorbi higueruelo nickolay baker-group
  • Dynamic personalities of proteins
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972.
    by Katherine Henzler-Wildman, Dorothee Kern
    posted to allostery experimental_methodology molecular_dynamics protein_folding protein-ligand_interactions by sobolevnrm on 2008-01-22 12:33:20 as read along with 15 people and 1 group viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
  • Modeling of metal interaction geometries for protein-ligand docking
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Birte Seebeck, Ingo Reulecke, Andreas Kämper, Matthias Rarey
    posted to bioinformatics metalloregulation protein-ligand_interactions by sobolevnrm on 2007-12-27 12:17:55 as read along with 1 person and 2 groups arlam group baker-group
  • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
    Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62.
    by JH Lin, AL Perryman, JR Schames, JA McCammon
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:47:44 as read along with 4 people and 3 groups barry blackbart kazemi LamBras structural_bioinformatics Bioinformatics baker-group
  • Molecular mechanics PBSA ligand binding energy and interaction of Efavirenz derivatives with HIV-1 reverse transcriptase
    Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 20, No. 2. (2005), pp. 129-134.
    by Philip Weinzinger, Sup Hannongbua, Pete Wolschann
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:43:25 as **
  • Intramolecular and Intermolecular Interactions of Protein Kinase B Define Its Activation In Vivo
    PLoS Biology, Vol. 5, No. 4. (1 April 2007), e95.
    by Véronique Calleja, Damien Alcor, Michel Laguerre, Jongsun Park, Borivoj Vojnovic, Brian A Hemmings, Julian Downward, Peter J Parker, Banafshé Larijani
    posted to electrostatics protein-ligand_interactions protein-protein_interactions structure by sobolevnrm on 2008-04-16 21:15:19 as read along with 1 group baker-group
  • Dynamics of Cholesterol Exchange in the Oxysterol Binding Protein Family
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Bertram J Canagarajah, Gerhard Hummer, William A Prinz, James H Hurley
    posted to oxysterols protein-ligand_interactions by sobolevnrm on 2008-05-03 12:32:00 as read along with 1 person and 1 group paulschlesinger baker-group
  • The Design and Evaluation of Heparin-Binding Foldamers
    Angewandte Chemie International Edition, Vol. 44, No. 41. (2005), pp. 6685-6689.
    by Sungwook Choi, Dylan J Clements, Vojislava Pophristic, Ivaylo Ivanov, Satyavani Vemparala, Joel S Bennett, Michael L Klein, Jeffrey D Winkler, William F Degrado
    posted to electrostatics protein_engineering protein_folding protein-ligand_interactions by sobolevnrm on 2008-04-16 21:11:55 as read along with 1 group baker-group
  • A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 155-164.
    by Andrew W Stumpff-Kane, Michael Feig
    posted to protein-ligand_interactions structure_prediction by sobolevnrm on 2007-12-18 13:05:11 as read along with 1 group baker-group
  • Binding similarity network of ligand
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Keunwan Park, Dongsup Kim
    posted to bioinformatics protein-ligand_interactions by sobolevnrm on 2007-12-20 12:31:21 as read along with 1 group baker-group
  • Alpha7 nicotinic acetylcholine receptor agonists: Prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Giovanni Grazioso, Andrea Cavalli, Marco De Amici, Maurizio Recanatini, Carlo De Micheli
    posted to apbs electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-06-30 11:30:07 as read along with 1 group baker-group
  • Flexible ligand-flexible protein docking in protein kinase systems
    Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1784, No. 1. (January 2008), pp. 244-251.
    by Chung F Wong
    posted to molecular_simulation protein-ligand_interactions drugdesign by sobolevnrm on 2008-01-18 16:34:38 as read along with 1 group baker-group
  • Divalent Cation Adsorption on the Actin Monomer
    J. Phys. Chem. C, Vol. 111, No. 43. (1 November 2007), pp. 15642-15652.
    by W Shi, MV Inamdar, AM Sastry, CM Lastoskie
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2007-10-29 11:25:37 as read along with 1 group baker-group
  • Engineering Protein Allostery: 1.05 Å Resolution Structure and Enzymatic Properties of a Na+-activated Trypsin
    Journal of Molecular Biology, Vol. 378, No. 3. (2 May 2008), pp. 666-672.
    by Michael J Page, Christopher J Carrell, Enrico Di Cera
    posted to allostery protein_engineering protein-ligand_interactions thrombin by sobolevnrm on 2008-05-03 12:32:51 as read along with 1 group baker-group
  • Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
    Journal of Computational Chemistry, Vol. 27, No. 16. (2006), pp. 1990-2007.
    by Christopher S Page, Paul A Bates
    posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 13:54:18 as read along with 1 group baker-group
  • A Mining Minima Approach to Exploring the Docking Pathways of p-Nitrocatechol Sulfate to YopH
    Biophys. J., Vol. 93, No. 12. (15 December 2007), pp. 4141-4150.
    by Zunnan Huang, Chung F Wong
    posted to protein-ligand_interactions by sobolevnrm on 2007-12-27 12:21:11 as read along with 1 group baker-group
  • Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
    J. Med. Chem. (18 June 2008)
    by Lily S Cheng, Rommie E Amaro, Dong Xu, Wilfred W Li, Peter W Arzberger, Andrew J Mccammon
    posted to apbs electrostatics protein-ligand_interactions drugdesign by sobolevnrm on 2008-06-21 02:55:07 as read along with 1 group baker-group
  • STITCH: interaction networks of chemicals and proteins.
    Nucleic Acids Res (15 December 2007)
    by Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl J Jensen, Peer Bork
    posted to bioinformatics database protein-ligand_interactions by sobolevnrm on 2008-01-24 12:53:09 as read along with 6 people and 1 group guhjy balicea massivemayhem bootsy larsjuhljensen higueruelo baker-group
  • Investigating interactions between HIV-1 gp41 and inhibitors by molecular dynamics simulation and MM-PBSA/GBSA calculations
    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 electrostatics protein-ligand_interactions solvation by sobolevnrm on 2008-04-16 14:11:48 as read along with 1 group baker-group
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to electrostatics molecular_simulation protein-ligand_interactions by sobolevnrm on 2008-06-13 11:49:09 as read along with 3 people and 3 groups jmccammon biehl barry baker-group structural_bioinformatics McCammon
  • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685.
    by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
    posted to electrostatics pka protein-ligand_interactions solvation by sobolevnrm on 2008-04-03 11:57:01 as read along with 4 people and 1 group mijogiffin dmobley sunhwan boris_aguilar baker-group
  • Three-Dimensional Distribution Function Theory for the Prediction of Protein-Ligand Binding Sites and Affinities: Application to the Binding of Noble Gases to Hen Egg-White Lysozyme in Aqueous Solution
    J. Phys. Chem. B (8 September 2007)
    by T Imai, R Hiraoka, T Seto, A Kovalenko, F Hirata
    posted to integral_equation protein-ligand_interactions solvation statistical_mechanics by sobolevnrm on 2007-09-10 12:41:47 as read along with 1 group baker-group
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