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chgjb's library [70 articles]

Recent papers added to chgjb's library.
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  • Generalized Crick equations for modeling noncanonical coiled coils.
    Journal of structural biology, Vol. 137, No. 1-2. (b 2002), pp. 41-53.
    by G Offer, MR Hicks, DN Woolfson
    posted to coile by chgjb on 2008-04-23 09:44:48 as **
  • A short history of SHELX
    Acta Crystallographica Section A Foundations of Crystallography
    by George M Sheldrick
    posted to crystal-structure by chgjb on 2008-04-02 13:47:20 as **
  • PROMOTIF--a program to identify and analyze structural motifs in proteins.
    Protein Sci, Vol. 5, No. 2. (February 1996), pp. 212-220.
    by EG Hutchinson, JM Thornton
    posted to program protein-structure-analysis by chgjb on 2008-03-26 15:00:40 as **
  • PISCES: a protein sequence culling server.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1589-1591.
    by G Wang, RL Dunbrack
    posted to database protein-sequence by chgjb on 2008-03-26 14:57:26 as ** along with 9 people and 2 groups reyez barry aalibes kaarsinogen j3xucite dgront blackbart mloewer ezralanglois structural_bioinformatics Bioinformatics
  • The occupancy of ions in the K+ selectivity filter: charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates.
    J Mol Biol, Vol. 333, No. 5. (7 November 2003), pp. 965-975.
    by Y Zhou, R MacKinnon
    posted to potassium-channel by chgjb on 2008-03-26 13:23:45 as **
  • Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0[thinsp][angst] resolution
    Nature, Vol. 414, No. 6859. (1 November 2001), pp. 43-48.
    by Yufeng Zhou, Joao H Morais-Cabral, Amelia Kaufman, Roderick Mackinnon
    posted to potassium-channel by chgjb on 2008-03-26 13:23:15 as ** along with 3 people and 2 groups nickle jwm jenni_p Radiation_Damage Stressosome
  • A survey of left-handed polyproline II helices.
    Protein Sci, Vol. 8, No. 3. (March 1999), pp. 587-595.
    by BJ Stapley, TP Creamer
    posted to prolines by chgjb on 2008-02-27 16:36:17 as **
  • Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects.
    Biopolymers, Vol. 61, No. 2., pp. 99-110.
    by A Bergner, J Günther, M Hendlich, G Klebe, M Verdonk
    posted to molecular-interactions by chgjb on 2008-02-27 11:42:24 as **
  • The interrelationships of side-chain and main-chain conformations in proteins.
    Prog Biophys Mol Biol, Vol. 76, No. 1-2. (2001), pp. 1-102.
    by P Chakrabarti, D Pal
    posted to molecular-interactions by chgjb on 2008-02-27 09:26:37 as ** along with 1 person blackbart
  • The nature of .pi.-.pi. interactions
    Journal of the American Chemical Society, Vol. 112, No. 14. (1990), pp. 5525-5534.
    by Christopher A Hunter, Jeremy KM Sanders
    posted to molecular-interactions by chgjb on 2008-02-27 09:20:14 as **
  • Weakly polar interactions in proteins.
    Adv Protein Chem, Vol. 39 (1988), pp. 125-189.
    by SK Burley, GA Petsko
    posted to molecular-interactions n-pi by chgjb on 2008-02-27 09:12:38 as **
  • Local and tunable n-->pi* interactions regulate amide isomerism in the peptoid backbone.
    J Am Chem Soc, Vol. 129, No. 29. (25 July 2007), pp. 8928-8929.
    by BC Gorske, BL Bastian, GD Geske, HE Blackwell
    posted to n-pi by chgjb on 2008-02-27 09:10:04 as **
  • Molecular torsion balances: evidence for favorable orthogonal dipolar interactions between organic fluorine and amide groups.
    Angew Chem Int Ed Engl, Vol. 46, No. 43. (2007), pp. 8270-8273.
    by FR Fischer, WB Schweizer, F Diederich
    posted to molecular-interactions by chgjb on 2008-02-27 09:09:21 as ** along with 1 person Lombardo_7
  • Orthogonal multipolar interactions in structural chemistry and biology.
    Angew Chem Int Ed Engl, Vol. 44, No. 12. (11 March 2005), pp. 1788-1805.
    by R Paulini, K Müller, F Diederich
    posted to molecular-interactions by chgjb on 2008-02-27 09:08:33 as **
  • Coulombic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands.
    J Mol Biol, Vol. 248, No. 2. (28 April 1995), pp. 374-384.
    by PH Maccallum, R Poet, EJ Milner-White
    posted to n-pi prolines by chgjb on 2008-02-27 09:01:12 as **
  • Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions.
    J Mol Biol, Vol. 248, No. 2. (28 April 1995), pp. 361-373.
    by PH Maccallum, R Poet, EJ Milner-White
    posted to n-pi prolines by chgjb on 2008-02-27 09:00:14 as **
  • Pyrrolidine ring puckering in cis and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations.
    J Mol Biol, Vol. 228, No. 3. (5 December 1992), pp. 725-734.
    by EJ Milner-White, LH Bell, PH Maccallum
    posted to n-pi prolines by chgjb on 2008-02-27 08:58:56 as **
  • Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations.
    J Am Chem Soc, Vol. 124, No. 11. (20 March 2002), pp. 2497-2505.
    by ML DeRider, SJ Wilkens, MJ Waddell, LE Bretscher, F Weinhold, RT Raines, JL Markley
    posted to n-pi by chgjb on 2008-02-27 08:56:22 as **
  • Non-proline Cis peptide bonds in proteins
    Journal of Molecular Biology, Vol. 286, No. 1. (February 1999), pp. 291-304.
    by Andreas Jabs, Manfred S Weiss, Rolf Hilgenfeld
    posted to cis-peptide protein-structure-analysis by chgjb on 2008-02-27 08:47:35 as **
  • An electronic effect on protein structure
    Protein Sci, Vol. 12, No. 6. (2003), pp. 1188-1194.
    by Matthew P Hinderaker, Ronald T Raines
    posted to n-pi protein-structure-analysis trans-cis by chgjb on 2008-02-27 08:47:35 as **
  • Energetics of an n --> pi interaction that impacts protein structure.
    Org Lett, Vol. 8, No. 21. (October 2006), pp. 4695-4697.
    by JA Hodges, RT Raines
    posted to n-pi protein-structure-analysis trans-cis by chgjb on 2008-02-27 08:47:35 as **
  • Atomic resolution density maps reveal secondary structure dependent differences in electronic distribution.
    J Am Chem Soc, Vol. 125, No. 42. (October 2003), pp. 12787-12794.
    by PI Lario, A Vrielink
    posted to electronic-distribution protein-structure-analysis by chgjb on 2008-02-27 08:47:35 as **
  • 2005 Emil Thomas Kaiser Award.
    Protein Sci, Vol. 15, No. 5. (May 2006), pp. 1219-1225.
    by RT Raines
    posted to collagen hydrogen-bonds protein-structure-analysis by chgjb on 2008-02-27 08:47:35 as **
  • The design of coiled-coil structures and assemblies.
    Adv Protein Chem, Vol. 70 (2005), pp. 79-112.
    by DN Woolfson
    posted to coiled-coil by chgjb on 2008-02-27 08:47:35 as **
  • Extended knobs-into-holes packing in classical and complex coiled-coil assemblies.
    J Struct Biol, Vol. 144, No. 3. (December 2003), pp. 349-361.
    by J Walshaw, DN Woolfson
    posted to coiled-coil knobs-into-holes socket by chgjb on 2008-02-27 08:47:35 as **
  • Socket: a program for identifying and analysing coiled-coil motifs within protein structures.
    J Mol Biol, Vol. 307, No. 5. (April 2001), pp. 1427-1450.
    by J Walshaw, DN Woolfson
    posted to coiled-coil knobs-into-holes protein-structure-analysis socket by chgjb on 2008-02-27 08:47:34 as **
  • The partial charge of the nitrogen atom in peptide bonds.
    Protein Sci, Vol. 6, No. 11. (November 1997), pp. 2477-2482.
    by EJ Milner-White
    posted to ni-pi by chgjb on 2008-02-25 18:03:42 as **
  • Preferred side-chain constellations at antiparallel coiled-coil interfaces
    No. 1091-6490 (Electronic).
    by Oliver, Derek, Samuel, SH Gellman
    posted to bibtex-import by chgjb on 2008-02-18 15:41:22 as **
  • FiberID--a technique to identify fibrous protein subclasses.
    Proteins, Vol. 66, No. 1. (1 January 2007), pp. 127-135.
    by P Waltman, A Blumer, D Kaplan
    posted to collagen computational-method by chgjb on 2008-02-18 09:24:26 as **
  • Coiled coil structures and transcription: an analysis of the S. cerevisiae coilome.
    Mol Genet Genomics (3 May 2007)
    by Kellie E Barbara, Kristine A Willis, Terry M Haley, Stephen J Deminoff, George M Santangelo
    posted to coilome genome-analysis by chgjb on 2008-02-18 09:23:20 as ** along with 1 person cjeans
  • An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1644-1649.
    by JA Barker, JM Thornton
    posted to 3d-templates by chgjb on 2008-02-06 15:40:50 as ** along with 6 people and 2 groups shadowman tjimenez jwm gbart tny siebertm Radiation_Damage Stressosome
  • Stabilizing and destabilizing clusters in the hydrophobic core of long two-stranded alpha-helical coiled-coils.
    J Biol Chem, Vol. 279, No. 20. (14 May 2004), pp. 21576-21588.
    by SC Kwok, RS Hodges
    posted to coiled-coil by chgjb on 2008-02-06 15:39:16 as **
  • Effect of chain length on coiled-coil stability: decreasing stability with increasing chain length.
    Biopolymers, Vol. 76, No. 5. (2004), pp. 378-390.
    by SC Kwok, RS Hodges
    posted to coiled-coil by chgjb on 2008-02-06 15:38:20 as **
  • Template-based coiled-coil antigens elicit neutralizing antibodies to the SARS-coronavirus.
    J Struct Biol, Vol. 155, No. 2. (August 2006), pp. 176-194.
    by B Tripet, DJ Kao, SA Jeffers, KV Holmes, RS Hodges
    posted to coiled-coil protein-design by chgjb on 2008-02-06 15:37:16 as **
  • Core Residue Replacements Cause Coiled-Coil Orientation Switching in Vitro and in Vivo: Structure-Function Correlations for Osmosensory Transporter ProP.
    Biochemistry (13 December 2007)
    by Yonit Tsatskis, Stanley C Kwok, Elisabeth Becker, Chad Gill, Michelle N Smith, Robert A Keates, Robert S Hodges, Janet M Wood
    posted to coiled-coil by chgjb on 2008-02-06 15:36:15 as ** along with 1 person cjeans
  • Deciphering B-ZIP transcription factor interactions in vitro and in vivo.
    Biochim Biophys Acta, Vol. 1759, No. 1-2. (b 2006), pp. 4-12.
    by C Vinson, A Acharya, EJ Taparowsky
    posted to bzip by chgjb on 2008-02-06 15:34:47 as ** along with 2 people cjeans gwenknight
  • Stability of 100 homo and heterotypic coiled-coil a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R).
    Biochemistry, Vol. 45, No. 38. (26 September 2006), pp. 11324-11332.
    by A Acharya, V Rishi, C Vinson
    posted to coiled-coil by chgjb on 2008-02-06 15:33:57 as ** along with 5 people gwenknight kevinchannon bethbromley ca3295 hmk
  • Peptide and non-peptide HIV fusion inhibitors.
    Curr Pharm Des, Vol. 8, No. 8. (2002), pp. 563-580.
    by S Jiang, Q Zhao, AK Debnath
    posted to gp41 by chgjb on 2008-02-06 15:32:47 as **
  • Covalent stabilization of coiled coils of the HIV gp41 N region yields extremely potent and broad inhibitors of viral infection.
    Proc Natl Acad Sci U S A, Vol. 102, No. 36. (6 September 2005), pp. 12903-12908.
    by E Bianchi, M Finotto, P Ingallinella, R Hrin, AV Carella, XS Hou, WA Schleif, MD Miller, R Geleziunas, A Pessi
    posted to gp41 by chgjb on 2008-02-06 15:32:17 as **
  • Protein design of a bacterially expressed HIV-1 gp41 fusion inhibitor.
    Biochemistry, Vol. 46, No. 14. (10 April 2007), pp. 4360-4369.
    by Y Deng, Q Zheng, TJ Ketas, JP Moore, M Lu
    posted to gp41 by chgjb on 2008-02-06 15:31:27 as **
  • Peptide mimic of the HIV envelope gp120-gp41 interface.
    J Mol Biol, Vol. 376, No. 3. (22 February 2008), pp. 786-797.
    by S Kim, HB Pang, MS Kay
    posted to gp41 by chgjb on 2008-02-06 15:28:12 as **
  • Rho GTPases: promising cellular targets for novel anticancer drugs.
    Curr Cancer Drug Targets, Vol. 6, No. 1. (February 2006), pp. 1-14.
    by G Fritz, B Kaina
    posted to gefs by chgjb on 2008-02-06 15:26:49 as **
  • Catching a GEF by its tail.
    Trends Cell Biol, Vol. 17, No. 1. (January 2007), pp. 36-43.
    by R García-Mata, K Burridge
    posted to gefs by chgjb on 2008-02-06 15:25:53 as ** along with 1 person jakub23
  • Structure-function based design of small molecule inhibitors targeting Rho family GTPases.
    Curr Top Med Chem, Vol. 6, No. 11. (2006), pp. 1109-1116.
    by N Nassar, J Cancelas, J Zheng, DA Williams, Y Zheng
    posted to gefs by chgjb on 2008-02-06 15:25:00 as **
  • Ultra-fast evaluation of protein energies directly from sequence.
    PLoS Comput Biol, Vol. 2, No. 6. (16 June 2006)
    by G Grigorya, F Zhou, SR Lustig, G Ceder, D Morgan, AE Keating
    posted to protein-energies protein-sequence by chgjb on 2008-02-06 15:23:02 as ** along with 1 person wouterboomsma
  • Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.
    Proc Natl Acad Sci U S A, Vol. 98, No. 26. (18 December 2001), pp. 14825-14830.
    by AE Keating, VN Malashkevich, B Tidor, PS Kim
    posted to prediction by chgjb on 2008-02-06 15:21:57 as **
  • Predicting specificity in bZIP coiled-coil protein interactions.
    Genome Biol, Vol. 5, No. 2. (2004)
    by JH Fong, AE Keating, M Singh
    posted to bzip prediction by chgjb on 2008-02-06 15:21:00 as ** along with 3 people cjeans hplatero gwenknight
  • Paircoil2: improved prediction of coiled coils from sequence.
    Bioinformatics, Vol. 22, No. 3. (1 February 2006), pp. 356-358.
    by AV McDonnell, T Jiang, AE Keating, B Berger
    posted to prediction by chgjb on 2008-02-06 15:20:28 as ** along with 1 person kgutwin
  • Structure-based prediction of bZIP partnering specificity.
    J Mol Biol, Vol. 355, No. 5. (3 February 2006), pp. 1125-1142.
    by G Grigoryan, AE Keating
    posted to bzip prediction by chgjb on 2008-02-06 15:19:50 as ** along with 4 people cjeans hplatero gwenknight ca3295
  • Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design.
    Proc Natl Acad Sci U S A, Vol. 103, No. 24. (13 June 2006), pp. 8989-8994.
    by JM Mason, MA Schmitz, KM Müller, KM Arndt
    posted to fos-jun protein-design by chgjb on 2008-02-06 15:18:19 as ** along with 3 people gwenknight bethbromley ca3295
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