Tag side-chain [70 articles] Export

Recent papers classified by the tag side-chain.

	Do Structurally Similar Ligands Bind in a Similar Fashion? [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6716-6725. by Jonas Bostrom, Anders Hogner, Stefan Schmitt posted to solvation similiarity side-chain sbdd protein_flexibility ligand flexibility drug_discovery 2006 by klexa on 2009-09-29 20:45:59 as along with 4 people schlauchi daevans superpyrin nickolay
	Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool [My Copy] Journal of Molecular Biology, Vol. 267, No. 5. (18 April 1997), pp. 1268-1282. by M. Bower posted to homology-modeling por-conseguir rotamer side-chain by carlosjavierna on 2009-08-08 06:05:20 as along with 6 people and 1 group kaarsinogen nknii blackbart mijam jwm carlk TCR_Signaling
	Extending the accuracy limits of prediction for side-chain conformations1 [My Copy] Journal of Molecular Biology, Vol. 311, No. 2. (10 August 2001), pp. 421-430. by Zhexin Xiang, Barry Honig posted to conformations honig-barry-h por-conseguir side-chain by carlosjavierna on 2009-08-08 04:23:29 as along with 1 person kazemi
	Backbone-dependent rotamer library for proteins. Application to side-chain prediction. [My Copy] Journal of molecular biology, Vol. 230, No. 2. (20 March 1993), pp. 543-574. by R. L. Dunbrack, M. Karplus posted to karplus-m rotamer rotamer-libraries side-chain by carlosjavierna on 2009-08-08 04:17:57 as along with 3 people and 1 group dfgreen nknii carlk TCR_Signaling
	Determinants of protein side-chain packing. [My Copy] Protein science : a publication of the Protein Society, Vol. 3, No. 12. (December 1994), pp. 2358-2365. by R. Tanimura, A. Kidera, H. Nakamura posted to side-chain by carlosjavierna on 2009-08-08 04:13:43 as along with 1 person carlk
	Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 46. (18 November 2008), pp. 17636-17641. by S. Vaitheeswaran, D. Thirumalai posted to side-chain by carlosjavierna on 2009-08-07 15:47:52 as along with 1 person kshundyak
	Computing protein stabilities from their chain lengths. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 26. (30 June 2009), pp. 10649-10654. by Kingshuk Ghosh, Ken A. Dill posted to dillka proteins side-chain by carlosjavierna on 2009-08-07 15:38:08 as along with 4 people kintoki apaydin sobolevnrm kevinchannon
	Hydration Free Energies of Amino Acids: Why Side Chain Analog Data Are Not Enough [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8967-8974. by Gerhard König, Stefan Boresch posted to amino-acid amino-acids free-energy side-chain by carlosjavierna on 2009-07-13 06:10:03 as along with 2 people flbarroso sobolevnrm
	Proton Affinities of Some Amino Acid Side Chains in a Restricted Environment [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 28. (16 July 2009), pp. 9570-9576. by T. G. Abi, Amit Anand, Srabani Taraphder posted to amino-acids side-chain by carlosjavierna on 2009-07-11 14:57:38 as
	Accurate Measurement of Methyl 13C Chemical Shifts by Solid-State NMR for the Determination of Protein Side Chain Conformation: The Influenza A M2 Transmembrane Peptide as an Example [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Mei Hong, Tatiana V. Mishanina, Sarah D. Cady posted to 13c protein side-chain ssnmr by viktor21614 on 2009-05-27 12:06:28 as
	Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 961-975. by Scott A. Showalter, Rafael Bruschweiler posted to dynamics md nmr prediction side-chain by pablocarb on 2009-04-19 16:06:22 as along with 3 people bmduggan allmensch loison
	Toward Quantitative Interpretation of Methyl Side-Chain Dynamics from NMR by Molecular Dynamics Simulations [My Copy] J. Am. Chem. Soc., Vol. 129, No. 46. (21 November 2007), pp. 14146-14147. by S. A. Showalter, E. Johnson, M. Rance, R. Bruschweiler posted to dynamics md methyl prediction side-chain by pablocarb on 2009-04-19 15:41:02 as along with 1 person and 1 group sobolevnrm baker-group
	Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 4. (2009), pp. 982-992. by Karel Berka, Roman Laskowski, Kevin E. Riley, Pavel Hobza, Jiří Vondrášek posted to amber force-field function interactions potential protein quantum_chemical residue-residue side-chain validation by krapnik on 2009-03-05 11:02:22 as along with 1 person carlosjavierna
	Using quantum mechanics to improve estimates of amino acid side chain rotamer energies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 4. (2008), pp. 1637-1646. by Douglas P. Renfrew, Glenn L. Butterfoss, Brian Kuhlman posted to conformation dft force-field hf mp2 quantum_chemical side-chain validation by krapnik on 2009-02-21 18:32:09 as along with 1 person Lombardo_7
	Effect of Mutation of Carboxyl Side-Chain Amino Acids Near the Heme on the Midpoint Potentials and Ligand Binding Constants of Nitrophorin 2 and Its NO, Histamine, and Imidazole Complexes [My Copy] Journal of the American Chemical Society, Vol. 131, No. 6. (18 February 2009), pp. 2313-2327. by Robert E. Berry, Maxim N. Shokhirev, Arthur Y. Ho, et al.Fei Yang, Tatiana K. Shokhireva, Hongjun Zhang, Andrzej Weichsel, William R. Montfort, Ann F. Walker posted to amino-acids mutation side-chain side-chain-amino-acids by carlosjavierna on 2009-02-20 04:47:55 as
	Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin [My Copy] ChemPhysChem, Vol. 10, No. 3. (2009), pp. 543-548. by Karel Berka, Pavel Hobza, Jiří Vondrášek posted to analysis dispersion interactions potential protein residue-residue side-chain by krapnik on 2009-02-16 09:01:58 as
	Computational protein design with side-chain conformational entropy [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 74, No. 1. (2009), pp. 176-191. by Daniele Sciretti, Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Pretti, Alfonso Jaramillo posted to side-chain structure_calculation by viktor21614 on 2009-02-05 15:52:10 as
	Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed [My Copy] Journal of the American Chemical Society, Vol. 130, No. 49. (10 December 2008), pp. 16611-16621. by Vipin Agarwal, Yi Xue, Bernd Reif, Nikolai R. Skrynnikov posted to amino_acid lnmr protein side-chain ssnmr by viktor21614 on 2008-12-09 11:47:58 as along with 2 people yxue mkrishna
	Statistical and conformational analysis of the electron density of protein side chains. [My Copy] Proteins, Vol. 66, No. 2. (1 February 2007), pp. 279-303. by M. V. Shapovalov, R. L. Dunbrack posted to protein side-chain by krapnik on 2008-11-28 13:49:10 as along with 1 person jwm
	Self-consistent estimation of interresidue protein contact energies based on an equilibrium mixture approximation of residues [My Copy] (1998) by S. Miyazawa posted to interactions potential protein residue-residue side-chain by krapnik on 2008-10-17 14:16:33 as along with 1 person iantunbridge
	Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes [My Copy] Protein Sci, Vol. 8, No. 2. (1 February 1999), pp. 361-369. by M. R. Betancourt, D. Thirumalai posted to interactions potential protein residue-residue side-chain by krapnik on 2008-10-17 14:16:04 as along with 1 person iantunbridge
	Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term [My Copy] (1996) by S. Miyazawa, R. Jernigan posted to interactions modeling potential protein residue-residue side-chain by krapnik on 2008-10-17 14:03:16 as along with 1 person iantunbridge
	Improved side-chain modeling for protein-protein docking. [My Copy] Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339. by C. Wang, O. Schueler-Furman, D. Baker posted to docking prediction protein side-chain by csrocha on 2008-10-08 05:36:25 as along with 11 people and 3 groups dgront barry aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
	Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients [My Copy] Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 34, No. 2. (19 March 1999), pp. 93-158. by Michael Sattler, Jurgen Schleucher, Christian Griesinger posted to nmr review side-chain triple-resonance by rph on 2008-04-23 18:28:12 as along with 2 people bmduggan laurabailey
	Linear viscoelasticity of side chain liquid crystal polymer [My Copy] Liquid Crystals, Vol. 13, No. 2. (1993), pp. 233-245. by R. H. Colby, J. R. Gillmor, G. Galli, M. Laus, C. K. Ober, E. Hall posted to liquid-crystal polymer side-chain viscoelastic by 39mick39 on 2008-04-21 06:08:55 as
	Stereospecific assignments of the isopropyl methyl groups of the membrane protein OmpX in DHPC micelles [My Copy] Journal of Biomolecular NMR, Vol. 27, No. 4. (1 December 2003), pp. 377-382. by Christian Hilty, Gerhard Wider, César Fernández, Kurt Wüthrich posted to imp nmr side-chain by rph on 2008-03-28 21:03:54 as
	Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO) [My Copy] Journal of Biomolecular NMR, Vol. 32, No. 3. (July 2005), pp. 219-233. by Hamid Eghbalnia, Arash Bahrami, Liya Wang, Amir Assadi, John Markley posted to assignments automation nmr proteomics side-chain by rph on 2008-03-28 01:14:26 as along with 1 person apaydin
	Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles [My Copy] Journal of Biomolecular NMR, Vol. 23, No. 4. (2002), pp. 289-301. by Christian Hilty, César Fernández, Gerhard Wider, Kurt Wüthrich posted to assignments imp nmr side-chain by rph on 2008-03-27 05:20:37 as
	Three-dimensional 1H-TOCSY-relayed ct-[13C,1H]-HMQC for aromatic spin system identification in uniformly 13C-labeled proteins [My Copy] Journal of Biomolecular NMR, Vol. 7, No. 2. (1 March 1996), pp. 99-106. by Oliver Zerbe, Thomas Szyperski, Marcel Ottiger, Kurt Wüthrich posted to aromatic assignments methods nmr side-chain by rph on 2008-03-21 21:42:19 as
	Bayesian statistical analysis of protein side-chain rotamer preferences. [My Copy] Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681. by R. L. Dunbrack, F. E. Cohen posted to packing protein side-chain by j3xucite on 2007-05-23 17:02:41 as along with 12 people and 2 groups karbak nknii dgront blackbart kazemi rsantana hmk LamBras mijam jwm phoenixzxl zwang MuraLab TCR_Signaling
	Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. [My Copy] J Comput Chem, Vol. 25, No. 5. (15 April 2004), pp. 712-724. by E. Eyal, R. Najmanovich, B. J. McConkey, M. Edelman, V. Sobolev posted to packing protein side-chain by j3xucite on 2007-02-19 18:59:22 as along with 3 people hryk blackbart mirzazadeh
	Rotamer libraries in the 21st century. [My Copy] Current opinion in structural biology, Vol. 12, No. 4. (August 2002), pp. 431-440. by Roland L. Dunbrack posted to side-chain by blackbart on 2006-07-24 21:28:04 as along with 9 people and 1 group bmduggan yongzhao dgront kazemi rsantana medic0747 LamBras mijam jwm TSRI_MGL
	Protein imperfections: separating intrinsic from extrinsic variation of torsion angles [My Copy] by Butterfoss posted to side-chain by blackbart on 2006-07-24 21:26:51 as along with 1 person martainn
	Analysis of side-chain orientations in homologous proteins. [My Copy] J Mol Biol, Vol. 196, No. 1. (5 July 1987), pp. 175-198. by N. L. Summers, W. D. Carlson, M. Karplus posted to side-chain by blackbart on 2006-07-24 21:25:36 as along with 1 person carlk
	Determinants of side chain conformational preferences in protein structures. [My Copy] Protein Eng, Vol. 11, No. 11. (November 1998), pp. 991-997. by R. Samudrala, J. Moult posted to side-chain by blackbart on 2006-07-24 21:24:10 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation1 [My Copy] Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1735-1747. by J.Michael Word,, Simon .. Lovell,, Jane .. Richardson,, David .. Richardson, posted to side-chain by blackbart on 2006-07-24 21:20:42 as along with 5 people and 2 groups ckmyo dfgreen kaarsinogen jwm j3xucite Radiation_Damage Stressosome
	The penultimate rotamer library. [My Copy] Proteins, Vol. 40, No. 3. (15 August 2000), pp. 389-408. by S. C. Lovell, J. M. Word, J. S. Richardson, D. C. Richardson posted to side-chain by blackbart on 2006-07-24 21:20:36 as along with 1 person and 2 groups jwm Radiation_Damage Stressosome
	Comparison of conformational characteristics in structurally similar protein pairs. [My Copy] Protein Sci, Vol. 2, No. 11. (November 1993), pp. 1811-1826. by T. P. Flores, C. A. Orengo, D. S. Moss, J. M. Thornton posted to side-chain by blackbart on 2006-07-24 21:18:30 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Side-chain conformational entropy at protein-protein interfaces. [My Copy] Protein Sci, Vol. 11, No. 12. (December 2002), pp. 2860-2870. by C. Cole, J. Warwicker posted to side-chain by blackbart on 2006-07-24 21:06:00 as
	The interrelationships of side-chain and main-chain conformations in proteins. [My Copy] Prog Biophys Mol Biol, Vol. 76, No. 1-2. (2001), pp. 1-102. by P. Chakrabarti, D. Pal posted to side-chain by blackbart on 2006-07-24 21:04:56 as along with 1 person chgjb
	Main-chain conformational features at different conformations of the side-chains in proteins [My Copy] Protein Eng., Vol. 11, No. 8. (1 August 1998), pp. 631-647. by P. Chakrabarti, D. Pal posted to side-chain by blackbart on 2006-07-24 21:04:43 as
	Boltzmann-type distribution of side-chain conformation in proteins. [My Copy] Protein Sci, Vol. 12, No. 12. (December 2003), pp. 2719-2731. by G. L. Butterfoss, J. Hermans posted to side-chain by blackbart on 2006-07-24 21:03:26 as along with 1 person ashaytan
	Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors [My Copy] Proteins: Structure, Function, and Genetics, Vol. 31, No. 2. (1998), pp. 201-213. by Oliviero Carugo, Patrick Argos posted to side-chain by blackbart on 2006-07-24 21:01:17 as
	Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction. [My Copy] Proteins, Vol. 37, No. 1. (1 October 1999), pp. 30-43. by J. Heringa, P. Argos posted to side-chain by blackbart on 2006-07-24 21:00:28 as along with 1 person carlk
	Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding. [My Copy] Proteins, Vol. 37, No. 1. (1 October 1999), pp. 44-55. by J. Heringa, P. Argos posted to side-chain by blackbart on 2006-07-24 21:00:23 as
	Correlation between side chain mobility and conformation in protein structures. [My Copy] Protein Eng, Vol. 10, No. 7. (July 1997), pp. 777-787. by O. Carugo, P. Argos posted to side-chain by blackbart on 2006-07-24 21:00:03 as
	Ligand-induced changes in the binding sites of proteins. [My Copy] Bioinformatics, Vol. 18, No. 7. (July 2002), pp. 939-948. by X. Fradera, X. De La Cruz, C. H. Silva, J. L. Gelpí, F. J. Luque, M. Orozco posted to side-chain by blackbart on 2006-07-24 20:58:33 as along with 1 person dgruiz
	Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. [My Copy] Biophys J, Vol. 84, No. 4. (April 2003), pp. 2273-2281. by T. M. Frimurer, G. H. Peters, L. F. Iversen, H. S. Andersen, N. P. Møller, O. H. Olsen posted to side-chain by blackbart on 2006-07-24 20:57:21 as along with 4 people and 1 group oteri dgruiz yongzhao kazemi TSRI_MGL
	Rotamers: To be or not to be? An Analysis of Amino Acid Side-chain Conformations in Globular Proteins [My Copy] Journal of Molecular Biology, Vol. 230, No. 2. (20 March 1993), pp. 592-612. by H. Schrauber posted to side-chain by blackbart on 2006-07-24 20:55:15 as along with 3 people carlosjavierna aqeel carlk
	Protein side-chain rearrangement in regions of point mutations. [My Copy] Proteins, Vol. 50, No. 2. (1 February 2003), pp. 272-282. by E. Eyal, R. Najmanovich, M. Edelman, V. Sobolev posted to side-chain by blackbart on 2006-07-24 20:53:37 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics

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protein	14
azobenzene	13
nmr	7
interactions	5
potential	5
residue-residue	5
docking	4
flexibility	4
liquid-crystal	4
photoresponsive	4
protein-ligand	4
synthesis	4
amino-acids	3
assignments	3
dynamics	3
methacrylate	3
prediction	3
alignment	2
birefringence	2
conformation	2
dichroic-dye	2
force-field	2
grating	2
imp	2
md	2
modeling	2
packing	2
polymer	2
por-conseguir	2
protein-protein	2
protein_flexibility	2
quantum_chemical	2
rotamer	2
sbdd	2
ssnmr	2
validation	2
13c	1
2006	1
2008	1
2009	1
algorithm	1
amber	1
amino-acid	1
amino_acid	1
analysis	1
aromatic	1
automation	1
binding_affinity	1
bioinformatics	1
ceboxy	1
conformations	1
de_novo	1
dft	1
dillka	1
dipole	1
dispersion	1
drug_discovery	1
free-energy	1
function	1
graft	1
helix	1
hf	1
homology-modeling	1
honig-barry-h	1
karplus-m	1
ligand	1
ligand-binding	1
ligand-docking	1
liquid-crystals	1
lnmr	1
loop	1
methods	1
methyl	1
molecular_dynamics	1
monomer	1
mp2	1
mutation	1
off-rotamer	1
polyethylene	1
proteins	1
proteomics	1
qsar	1
raft	1
review	1
rotamer-libraries	1
scaffold	1
screening	1
side-chain-amino-acids	1
similiarity	1
solvation	1
structure	1
structure_calculation	1
supramolecule	1
surfactant	1
transition	1
triple-resonance	1
virtual-screening	1
viscoelastic	1

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