Group: structural_bioinformatics - with tag protein_protein [63 articles] Export

Recent papers posted by members of the structural_bioinformatics group with tag protein_protein

	Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta [My Copy] Journal of Molecular Biology (08 July 2009) by Frank Dimaio, Michael D. Tyka, Matthew L. Baker, Wah Chiu, David Baker posted to cryo_em protein_protein by barry to the group structural_bioinformatics on 2009-07-26 09:05:37 as along with 2 people and 1 group apaydin reyez McCammon
	Fruitful and Futile Encounters along the Association Reaction between Proteins [My Copy] Biophysical Journal, Vol. 96, No. 10. (20 May 2009), pp. 4237-4248. by Michal Harel, Alexander Spaar, Gideon Schreiber posted to brownian_dynamics diffusion electrostatics protein_protein by barry to the group structural_bioinformatics on 2009-06-23 23:55:06 as along with 1 person and 1 group jmccammon McCammon
	FireDock: a web server for fast interaction refinement in molecular docking [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W229-232. by Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, Haim J. Wolfson posted to docking_refinement protein_protein by barry to the group structural_bioinformatics on 2009-06-18 20:29:10 as
	Replica exchange simulations of transient encounter complexes in protein–protein association [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 35. (2 September 2008), pp. 12855-12860. by Young C. Kim, Chun Tang, G. Marius Clore, Gerhard Hummer posted to protein_protein by barry to the group structural_bioinformatics on 2009-06-11 20:08:20 as along with 2 people and 1 group okapi cactus McCammon
	Prediction of Protein-Protein Association Rates from a Transition-State Theory [My Copy] Structure, Vol. 15, No. 2. (February 2007), pp. 215-224. by R. Alsallaq, H. Zhou posted to bd_simulation electrostatics protein_protein by barry to the group structural_bioinformatics on 2009-03-13 18:41:54 as along with 2 people and 1 group apaydin flbarroso McCammon
	A survey of available tools and web servers for analysis of protein-protein interactions and interfaces [My Copy] Brief Bioinform, Vol. 10, No. 3. (1 May 2009), pp. 217-232. by Nurcan Tuncbag, Gozde Kar, Ozlem Keskin, Attila Gursoy, Ruth Nussinov posted to protein_protein review server by barry to the group structural_bioinformatics on 2009-03-04 04:46:11 as along with 12 people and 2 groups dfdong jinghu_fandm daforerog qluo SaraNasser mikaellund reyez diamantis apaydin semin renatomilani svozil McCammon Bioinformatics
	Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (5 February 2009) by James R R. Horn, Tobin R R. Sosnick, Anthony A A. Kossiakoff posted to protein_protein by barry to the group structural_bioinformatics on 2009-02-09 06:48:08 as along with 2 people and 1 group amishp higueruelo McCammon
	Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests [My Copy] PLoS Comput Biol, Vol. 5, No. 1. (30 January 2009), e1000278. by Mile Šikić, Sanja Tomić, Kristian Vlahoviček posted to protein_protein protein_sequence by barry to the group structural_bioinformatics on 2009-02-05 23:50:40 as along with 7 people and 1 group roys svozil marti grahamc higueruelo kshameer neils McCammon
	Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles [My Copy] Journal of Molecular Biology, Vol. 381, No. 4. (12 September 2008), pp. 1068-1087. by S. Chaudhury, J. Gray posted to conformational_selection docking protein_protein by barry to the group structural_bioinformatics on 2008-12-02 18:12:27 as along with 1 group McCammon
	2D depiction of nonbonding interactions for protein complexes. [My Copy] Journal of computational chemistry (22 October 2008) by Peng Zhou, Feifei Tian, Zhicai Shang posted to bioinf_methods protein_protein by barry to the group structural_bioinformatics on 2008-10-25 17:59:23 as along with 2 people and 2 groups whitead higueruelo Jiang Research Group McCammon
	Protein co-evolution, co-adaptation and interactions. [My Copy] The EMBO journal, Vol. 27, No. 20. (22 October 2008), pp. 2648-2655. by Florencio Pazos, Alfonso Valencia posted to correlated_mutations phylogeny protein_protein review by barry to the group structural_bioinformatics on 2008-10-02 20:24:17 as along with 8 people and 2 groups chica biomcgary qluo balicea grahamc fhsantanna marti sjcockell McCammon Bioinformatics
	Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Anthony A. Kossiakoff, Shohei Koide posted to protein_dynamics protein_protein review by barry to the group structural_bioinformatics on 2008-10-02 19:21:02 as along with 2 people and 2 groups grahamc paulschlesinger McCammon Bioinformatics
	A Specificity Map for the PDZ Domain Family [My Copy] PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239. by Raffi Tonikian, Yingnan Zhang, Stephen L. Sazinsky, et al.Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A. Held, Brent A. Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C. Chan, Somasekar Seshagiri, Laurence A. Lasky, Chris Sander, Charles Boone, Gary D. Bader, Sachdev S. Sidhu posted to pdz protein_protein by barry to the group structural_bioinformatics on 2008-09-30 18:44:35 as along with 6 people and 2 groups kgutwin balicea grahamc markchen zwang cabbagesofdoom McCammon Bioinformatics
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted to comparative_model protein_protein protein_structure by barry to the group structural_bioinformatics on 2008-08-01 19:03:07 as along with 18 people and 2 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF
	Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding [My Copy] Journal of Molecular Biology, Vol. 375, No. 5. (01 February 2008), pp. 1416-1433. by Young C. Kim, Gerhard Hummer posted to coarse-grained protein_protein ubiqutin by barry to the group structural_bioinformatics on 2008-01-10 19:41:25 as along with 4 people and 2 groups okapi sobolevnrm iantunbridge mikaellund Bioinformatics baker-group
	Complementarity of Structure Ensembles in Protein-Protein Binding [My Copy] Structure, Vol. 12, No. 12. (December 2004), pp. 2125-2136. by Raik Gruenberg, Johan Leckner, Michael Nilges posted to md_simulation protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2007-10-02 03:05:14 as along with 4 people and 2 groups raik lna allmensch cursonivel1 Bioinformatics cursonivel1
	Assessing predictions of protein-protein interaction: the CAPRI experiment. [My Copy] Protein Sci, Vol. 14, No. 2. (February 2005), pp. 278-283. by J. Janin posted to docking protein_protein by barry to the group structural_bioinformatics on 2007-09-27 19:26:18 as along with 5 people mkotlyar csrocha bicko ima drastic
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to docking protein_protein by barry to the group structural_bioinformatics on 2007-09-27 17:40:34 as along with 6 people and 1 group mijam kgutwin csrocha jwm xdeupi Ema Bioinformatics
	Localization of protein-binding sites within families of proteins. [My Copy] Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360. by D. Korkin, F. P. Davis, A. Sali posted to protein_structure protein_sequence protein_protein by barry to the group structural_bioinformatics on 2007-09-14 01:51:37 as along with 4 people and 3 groups tjimenez bicko marcius wilbur Bioinformatics BioinfoCIPF SGU-CIPF
	How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. [My Copy] Biophys J, Vol. 88, No. 3. (March 2005), pp. 1552-1559. by T. Haliloglu, O. Keskin, B. Ma, R. Nussinov posted to protein_structure protein_protein nma by barry to the group structural_bioinformatics on 2007-09-13 18:55:42 as along with 4 people and 1 group baaden aqeel eweaver choonpeng Bioinformatics
	Dehydron: a structurally encoded signal for protein interaction. [My Copy] Biophys J, Vol. 85, No. 3. (September 2003), pp. 1914-1928. by A. Fernández, R. Scott posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group structural_bioinformatics on 2007-09-13 18:45:52 as along with 4 people and 1 group marti dkoveal BragilMassoud Evangelia Bioinformatics
	Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. [My Copy] Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 113-118. by A. Fernández, H. A. Scheraga posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group structural_bioinformatics on 2007-09-13 18:45:36 as along with 3 people and 1 group marti dkoveal BragilMassoud Bioinformatics
	Amino acid preferences at protein binding sites [My Copy] FEBS Letters, Vol. 349, No. 1. (25 July 1994), pp. 125-130. by Hugo O. Villar, Lawrence M. Kauvar posted to protein_sequence protein_protein by barry to the group structural_bioinformatics on 2007-09-04 20:17:20 as along with 1 group Bioinformatics
	Association of putative concave protein-binding sites with the fluctuation behavior of residues. [My Copy] Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2265-2277. by A. Ertekin, R. Nussinov, T. Haliloglu posted to protein_protein protein_dynamics nma by barry to the group structural_bioinformatics on 2007-09-04 20:13:14 as along with 1 person and 1 group aqeel Bioinformatics
	Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. [My Copy] 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 protein_structure protein_sequence protein_protein hot_spots by barry to the group structural_bioinformatics on 2007-09-04 19:49:40 as along with 10 people and 1 group tbinbal dkoveal mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab Bioinformatics
	Optimization of specificity in a cellular protein interaction network by negative selection. [My Copy] Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680. by A. Zarrinpar, S. H. Park, W. A. Lim posted to protein_structure protein_sequence protein_protein protein_evolution protein_design by barry to the group structural_bioinformatics on 2007-09-04 19:25:04 as along with 4 people and 1 group grahamc cjeans paolomarcatili phoenixzxl Bioinformatics
	Conformational entropy in molecular recognition by proteins [My Copy] Nature, Vol. 448, No. 7151. (2007), pp. 325-9. by K. K. Frederick, M. S. Marlow, K. G. Valentine, A. J. Wand posted to protein_protein protein_ligand nmr by barry to the group structural_bioinformatics on 2007-08-28 02:08:20 as along with 1 person and 2 groups sobolevnrm Bioinformatics baker-group
	Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. [My Copy] J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795. by X. Li, O. Keskin, B. Ma, R. Nussinov, J. Liang posted to protein_protein by barry to the group structural_bioinformatics on 2007-08-14 22:53:26 as along with 10 people and 1 group baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab paolomarcatili Bioinformatics
	Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 20. (15 May 2007), pp. 8311-8315. by Vincent J. Hilser, E. Brad Thompson posted to protein_structure protein_protein protein_dynamics disorder allosteric by barry to the group structural_bioinformatics on 2007-05-25 01:36:39 as along with 6 people and 2 groups guhjy apaydin choonpeng cursonivel1 cactus allmensch Bioinformatics cursonivel1
	Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 25. (22 June 2004), pp. 9223-9228. by C. Kiel, T. Selzer, Y. Shaul, G. Schreiber, C. Herrmann posted to ras protein_protein electrostatics bd_simulation by barry to the group structural_bioinformatics on 2007-01-16 23:20:45 as along with 1 group Bioinformatics
	Insights into Protein–Protein Interfaces using a Bayesian Network Prediction Method [My Copy] Journal of Molecular Biology, Vol. 362, No. 2. (15 September 2006), pp. 365-386. by James R. Bradford, Chris J. Needham, Andrew J. Bulpitt, David R. Westhead posted to bayesian_classifiers bioinf_methods protein_protein by barry to the group structural_bioinformatics on 2006-08-28 18:00:47 as along with 8 people and 1 group dfdong conkymacro ameetsoni grahamc massivemayhem phoenixzxl marti paolomarcatili Bioinformatics
	Structural diversity of domain superfamilies in the CATH database. [My Copy] Journal of molecular biology, Vol. 360, No. 3. (14 July 2006), pp. 725-741. by Gabrielle A. Reeves, Timothy J. Dallman, Oliver C. Redfern, Adrian Akpor, Christine A. Orengo posted to cath protein_design protein_evolution protein_protein protein_structure by barry to the group structural_bioinformatics on 2006-07-07 19:57:04 as along with 4 people and 4 groups martainn yuslinaz marcius sobolevnrm Bioinformatics BioinfoCIPF SGU-CIPF baker-group
	Flexibility and conformational entropy in protein-protein binding. [My Copy] Structure, Vol. 14, No. 4. (April 2006), pp. 683-693. by R. Grünberg, M. Nilges, J. Leckner posted to md_simulation protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2006-05-22 19:20:49 as along with 6 people and 1 group hmk raik pansapiens lna aqeel allmensch Bioinformatics
	Flexibility and conformational entropy in protein-protein binding [My Copy] Structure (London, England: 1993), Vol. 14, No. 4. (April 2006), pp. 683-693. by Raik Grunberg, Michael Nilges, Johan Leckner posted to md_simulation protein_dynamics protein_protein protein_structure by barry to the group structural_bioinformatics on 2006-05-08 20:05:12 as along with 1 person and 4 groups joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. [My Copy] Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3360-3368. by J. Espadaler, O. Romero-Isart, R. M. Jackson, B. Oliva posted to protein_protein protein_sequence protein_structure sequence_comparison structure_comparison by barry to the group structural_bioinformatics on 2006-03-06 22:20:06 as along with 2 people and 1 group bicko baldo Bioinformatics
	Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. [My Copy] Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2850-2855. by A. S. Aytuna, A. Gursoy, O. Keskin posted to bioinf_methods protein_protein protein_sequence protein_structure by barry to the group structural_bioinformatics on 2006-03-06 22:03:40 as along with 4 people and 1 group apaydin bicko j3xucite dyermd Bioinformatics
	Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. [My Copy] J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502. by R. Landgraf, I. Xenarios, D. Eisenberg posted to protein_design protein_protein protein_sequence protein_structure residue_annotation by barry to the group structural_bioinformatics on 2006-03-02 22:37:16 as along with 8 people and 1 group dfdong ramiro2k pansapiens sriram_s cjeans mingzhi Pao-Yang marti Bioinformatics
	Computational Alanine Scanning of Protein-Protein Interfaces [My Copy] Sci. STKE, Vol. 2004, No. 219. (10 February 2004), pl2. by Tanja Kortemme, David E. Kim, David Baker posted to bioinf_methods protein_protein protein_structure by barry to the group structural_bioinformatics on 2005-12-07 23:56:00 as along with 8 people and 5 groups chemrahul82 onufriev pablocarb bicko sangeetha blackbart joergkurtwegner skoddet Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	Protein-protein interactions: a review of protein dimer structures. [My Copy] Prog Biophys Mol Biol, Vol. 63, No. 1. (1995), pp. 31-65. by S. Jones, J. M. Thornton posted to bioinf_methods protein_protein protein_structure review by barry to the group structural_bioinformatics on 2005-12-07 23:47:30 as along with 4 people and 4 groups viktor21614 bicko chad_davis joergkurtwegner Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Structure, function, and evolution of transient and obligate proteinâprotein interactions [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 31. (2 August 2005), pp. 10930-10935. by Julian Mintseris, Zhiping Weng posted to protein_protein review by barry to the group structural_bioinformatics on 2005-10-17 18:55:00 as along with 12 people and 2 groups dfdong timg mgomes bjorns wiehe julianm bicko chad_davis cjeans Evangelia marti higueruelo ZLAB Bioinformatics
	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 protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2005-10-17 18:53:58 as along with 11 people and 2 groups dgront csrocha aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia Bioinformatics TSRI_MGL
	Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194. by O. Schueler-Furman, C. Wang, D. Baker posted to bioinf_methods protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2005-10-17 18:52:59 as along with 3 people and 1 group jwm bicko bluvsh1 Bioinformatics
	Anchor residues in protein–protein interactions [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 31. (3 August 2004), pp. 11287-11292. by Deepa Rajamani, Spencer Thiel, Sandor Vajda, Carlos J. Camacho posted to protein_protein by barry to the group structural_bioinformatics on 2005-10-17 18:51:04 as along with 5 people and 1 group mikaellund dkoveal bicko bluvsh1 boris_aguilar Bioinformatics
	Soft protein-protein docking in internal coordinates. [My Copy] Protein Sci, Vol. 11, No. 2. (February 2002), pp. 280-291. by J. Fernández-Recio, M. Totrov, R. Abagyan posted to bioinf_methods protein_protein by barry to the group structural_bioinformatics on 2005-10-17 18:49:54 as along with 5 people and 1 group bicko bluvsh1 cjeans selrac wilbur Bioinformatics
	Statistical analysis and prediction of protein-protein interfaces [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3. (19 May 2005), pp. 353-366. by Andrew J. Bordner, Ruben Abagyan posted to bioinf_methods protein_protein svm by barry to the group structural_bioinformatics on 2005-10-17 18:44:16 as along with 8 people and 1 group dfdong boris_aguilar bicko lyongu ameetsoni cjeans Evangelia marti Bioinformatics
	Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. [My Copy] J Med Chem, Vol. 48, No. 13. (30 June 2005), pp. 4432-4443. by X. Barril, S. D. Morley posted to protein_dynamics protein_protein by barry to the group structural_bioinformatics on 2005-10-08 00:59:52 as along with 3 people and 2 groups BragilMassoud apaydin yongzhao Bioinformatics TSRI_MGL
	Processivity of the single-headed kinesin KIF1A through biased binding to tubulin. [My Copy] Nature, Vol. 424, No. 6948. (31 July 2003), pp. 574-577. by Y. Okada, H. Higuchi, N. Hirokawa posted to kif1a kinesin molecular_motors protein_protein tubulin by barry to the group structural_bioinformatics on 2005-06-24 23:26:22 as along with 1 person and 1 group qwermish Bioinformatics
	KIF1A alternately uses two loops to bind microtubules. [My Copy] Science, Vol. 305, No. 5684. (30 July 2004), pp. 678-683. by R. Nitta, M. Kikkawa, Y. Okada, N. Hirokawa posted to kif1a kinesin molecular_motors protein_protein by barry to the group structural_bioinformatics on 2005-06-24 23:23:02 as along with 2 people and 1 group shuns qwermish Bioinformatics
	Modulation of kinesin binding by the C-termini of tubulin. [My Copy] EMBO J, Vol. 23, No. 5. (10 March 2004), pp. 989-999. by G. Skiniotis, J. C. Cochran, J. Müller, E. Mandelkow, S. P. Gilbert, A. Hoenger posted to kinesin molecular_motors protein_protein tubulin by barry to the group structural_bioinformatics on 2005-06-24 23:20:59 as along with 1 group Bioinformatics
	Structure-based systems biology: a zoom lens for the cell. [My Copy] FEBS Lett, Vol. 579, No. 8. (21 March 2005), pp. 1854-1858. by P. Aloy, R. B. Russell posted to bioinformatics gotit protein_protein review structural_bioinformatics systems_biology by barry to the group structural_bioinformatics on 2005-04-25 22:46:34 as along with 4 people and 1 group karbak lyongu biosv chad_davis Bioinformatics

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protein_structure	64
structural_bioinformatics	41
bioinf_methods	30
protein_sequence	30
protein_dynamics	29
review	25
gotit	21
md_simulation	12
protein_design	11
kinesin	10
molecular_motors	10
docking	8
electrostatics	8
tubulin	8
bd_simulation	7
correlated_mutations	7
bioinformatics	6
dehydron	6
hbond	6
kif1a	6
nma	6
protein_evolution	6
protein_packing	6
sequence_comparison	6
pdz	5
server	5
phylogeny	4
allosteric	3
bayesian_classifiers	3
cath	3
coarse-grained	3
conformational_selection	3
cryo_em	3
disorder	3
hot_spots	3
interaction_maps	3
ras	3
residue_annotation	3
structure_comparison	3
svm	3
systems_biology	3
ubiqutin	3
brownian_dynamics	2
comparative_model	2
diffusion	2
docking_refinement	2
mts	2
epr	1
protein_ligand	1
textmining	1

Group: structural_bioinformatics - with tag protein_protein [63 articles] Export

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