barry's protein_protein [77 articles] Export

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	Computational design of affinity and specificity at protein–protein interfaces [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 4. (29 August 2009), pp. 458-463. by John Karanicolas, Brian Kuhlman posted to protein_protein review by barry on 2009-08-06 23:48:47 as along with 4 people bmduggan sobolevnrm VGreiff higueruelo
	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 on 2009-07-26 09:05:37 as along with 2 people and 2 groups apaydin reyez structural_bioinformatics 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 on 2009-06-23 23:55:06 as along with 1 person and 2 groups jmccammon structural_bioinformatics 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 on 2009-06-18 20:29:10 as along with 1 group structural_bioinformatics
	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 on 2009-06-11 20:08:19 as along with 2 people and 2 groups okapi cactus structural_bioinformatics McCammon
	Fundamental Aspects of Protein−Protein Association Kinetics [My Copy] Chemical Reviews, Vol. 109, No. 3. (11 March 2009), pp. 839-860. by G. Schreiber, G. Haran, H. X. Zhou posted to bd_simulation protein_protein by barry on 2009-04-21 08:24:42 as along with 10 people and 2 groups anuragsethi sunhwan jmccammon sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger McCammon baker-group
	Progress and challenges in predicting protein-protein interaction sites [My Copy] Brief Bioinform, Vol. 10, No. 3. (1 May 2009), pp. 233-246. by Iakes Ezkurdia, Lisa Bartoli, Piero Fariselli, Rita Casadio, Alfonso Valencia, Michael L. Tress posted to protein_protein review by barry on 2009-04-21 07:51:52 as along with 9 people and 1 group flbarroso biomcgary nanonan apaydin marti neils reyez renatomilani iakes McCammon
	Graphical models of protein-protein interaction specificity from correlated mutations and interaction data [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2 February 2009), pp. 911-929. by John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg posted to correlated_mutations pdz protein_protein by barry on 2009-03-25 21:58:54 as along with 5 people and 2 groups dfdong sobolevnrm AliC qluo RebeccaHamer Orengo Group Journal Picks baker-group
	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 on 2009-03-13 18:41:53 as along with 2 people and 2 groups apaydin flbarroso structural_bioinformatics 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 on 2009-03-04 04:46:11 as along with 12 people and 3 groups dfdong jinghu_fandm daforerog qluo SaraNasser mikaellund reyez diamantis apaydin semin renatomilani svozil structural_bioinformatics McCammon Bioinformatics
	ProtorP: A Protein-Protein Interaction Analysis Server [My Copy] Bioinformatics (11 November 2008), btn584. by Christopher Reynolds, David Damerell, Susan Jones posted to protein_protein server by barry on 2009-02-12 07:03:05 as along with 7 people and 1 group idoerg bicko chad_davis behindtherabbit neils kshameer hugowill structural_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 on 2009-02-09 06:48:08 as along with 2 people and 2 groups amishp higueruelo structural_bioinformatics 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 on 2009-02-05 23:50:40 as along with 7 people and 2 groups roys svozil marti grahamc higueruelo kshameer neils structural_bioinformatics McCammon
	Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree [My Copy] Journal of Molecular Biology, Vol. 385, No. 1. (09 January 2009), pp. 91-98. by M. Kann, B. Shoemaker, A. Panchenko, T. Przytycka posted to correlated_mutations protein_protein by barry on 2009-01-10 02:15:22 as along with 11 people and 2 groups mgomes biomcgary chica druvus sobolevnrm mhofree grahamc zwang marti reyez paulschlesinger baker-group Bioinformatics
	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 on 2008-12-02 18:12:27 as along with 2 groups structural_bioinformatics 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_ligand protein_protein by barry on 2008-10-25 17:59:22 as along with 2 people and 3 groups whitead higueruelo Jiang Research Group structural_bioinformatics McCammon
	Computational Design of Calmodulin Mutants with up to 900-Fold Increase in Binding Specificity. [My Copy] Journal of molecular biology (27 September 2008) by Eliyahu Yosef, Regina Politi, Mee H H. Choi, Julia M M. Shifman posted to protein_design protein_protein by barry on 2008-10-12 08:12:04 as along with 2 people and 1 group msuarezdiez higueruelo 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 on 2008-10-02 20:24:17 as along with 8 people and 3 groups chica biomcgary qluo balicea grahamc fhsantanna marti sjcockell structural_bioinformatics McCammon Bioinformatics
	Progress and challenges in protein structure prediction [My Copy] Current Opinion in Structural Biology In Nucleic acids / Sequences and topology, Vol. 18, No. 3. (June 2008), pp. 342-348. by Y. Zhang posted to protein_protein review by barry on 2008-10-02 19:37:50 as along with 11 people saunders ameetsoni rodrigofaccioli jperkins newton1234 hadesnumb kgutwin chad_davis phoenixzxl marck zwang
	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 on 2008-10-02 19:21:01 as along with 2 people and 3 groups grahamc paulschlesinger structural_bioinformatics 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 on 2008-09-30 18:44:35 as along with 6 people and 3 groups kgutwin balicea grahamc markchen zwang cabbagesofdoom structural_bioinformatics 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 on 2008-08-01 19:03:06 as along with 18 people and 3 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF structural_bioinformatics
	Conformational dynamics of loops L11 and L12 of kinesin as revealed by spin-labeling EPR [My Copy] Biochemical and Biophysical Research Communications, Vol. 364, No. 3. (21 December 2007), pp. 620-626. by Masafumi D. Yamada, Shinsaku Maruta, Satoshi Yasuda, Kazunori Kondo, Hidekatsu Maeda, Toshiaki Arata posted to epr kinesin molecular_motors protein_protein by barry on 2008-06-02 19:35:08 as
	A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis [My Copy] PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98. by Julian R. Hughes, Ana M. Meireles, Katherine H. Fisher, et al.Angel Garcia, Philip R. Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G. Wakefield posted to mts protein_protein tubulin by barry on 2008-04-29 19:37:04 as along with 1 person and 1 group cdeane Bioinformatics
	Protein interactions in human genetic diseases [My Copy] Genome Biology, Vol. 9, No. 1. (2008) by Benjamin S. Bockler, Alex Bateman posted to protein_protein protein_structure by barry on 2008-03-20 01:10:21 as along with 10 people and 2 groups balicea frohike neils grahamc aconesa biomcgary barriot mingzhi mclarenv guhjy Bioinformatics McCammon
	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 on 2008-01-10 19:41:24 as along with 4 people and 3 groups okapi sobolevnrm iantunbridge mikaellund structural_bioinformatics 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 on 2007-10-02 03:05:14 as along with 4 people and 3 groups raik lna allmensch cursonivel1 structural_bioinformatics 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 on 2007-09-27 19:26:18 as along with 5 people and 1 group mkotlyar csrocha bicko ima drastic structural_bioinformatics
	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 on 2007-09-27 17:40:34 as along with 6 people and 2 groups mijam kgutwin csrocha jwm xdeupi Ema structural_bioinformatics 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_protein protein_sequence protein_structure by barry on 2007-09-14 01:51:37 as along with 4 people and 4 groups tjimenez bicko marcius wilbur structural_bioinformatics 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 nma protein_protein protein_structure by barry on 2007-09-13 18:55:42 as along with 4 people and 2 groups baaden aqeel eweaver choonpeng structural_bioinformatics 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 dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:52 as along with 4 people and 2 groups marti dkoveal BragilMassoud Evangelia structural_bioinformatics 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 dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:36 as along with 3 people and 2 groups marti dkoveal BragilMassoud structural_bioinformatics 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_protein protein_sequence by barry on 2007-09-04 20:17:20 as along with 2 groups structural_bioinformatics 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 nma protein_dynamics protein_protein by barry on 2007-09-04 20:13:14 as along with 1 person and 2 groups aqeel structural_bioinformatics 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 hot_spots protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:49:40 as along with 10 people and 2 groups tbinbal dkoveal mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics 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_design protein_evolution protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:25:04 as along with 4 people and 2 groups grahamc cjeans paolomarcatili phoenixzxl structural_bioinformatics 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 nmr protein_ligand protein_protein by barry on 2007-08-28 02:08:20 as along with 1 person and 3 groups sobolevnrm structural_bioinformatics 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 on 2007-08-14 22:53:26 as along with 10 people and 2 groups baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab paolomarcatili structural_bioinformatics 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 allosteric disorder protein_dynamics protein_protein protein_structure by barry on 2007-05-25 01:36:39 as along with 6 people and 3 groups guhjy apaydin choonpeng cursonivel1 cactus allmensch structural_bioinformatics 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 on 2007-01-16 23:20:45 as along with 2 groups structural_bioinformatics Bioinformatics
	Interrogating protein interaction networks through structural biology [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901. by Patrick Aloy, Robert B. Russell posted to protein_protein protein_structure by barry on 2006-09-29 19:14:25 as along with 15 people and 3 groups beete aceol kgutwin tomhebbron bpcusack ana baaden bicko lfriedl chad_davis henschel ruvido cjeans tale Evangelia structural_bioinformatics kdl 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 on 2006-08-28 18:00:47 as along with 8 people and 2 groups dfdong conkymacro ameetsoni grahamc massivemayhem phoenixzxl marti paolomarcatili structural_bioinformatics 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 on 2006-07-07 19:57:04 as along with 4 people and 5 groups martainn yuslinaz marcius sobolevnrm structural_bioinformatics 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 on 2006-05-22 19:20:49 as along with 6 people and 2 groups hmk raik pansapiens lna aqeel allmensch structural_bioinformatics 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 on 2006-05-08 20:05:12 as along with 1 person and 5 groups joergkurtwegner structural_bioinformatics 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 on 2006-03-06 22:20:06 as along with 2 people and 2 groups bicko baldo structural_bioinformatics 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 on 2006-03-06 22:03:40 as along with 4 people and 2 groups apaydin bicko j3xucite dyermd structural_bioinformatics 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 on 2006-03-02 22:37:16 as along with 7 people and 2 groups ramiro2k pansapiens sriram_s cjeans mingzhi Pao-Yang marti structural_bioinformatics 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 on 2005-12-07 23:56:00 as along with 8 people and 6 groups chemrahul82 onufriev pablocarb bicko sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug

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protein_structure	278
molecular_motors	190
review	190
kinesin	145
protein_dynamics	132
md_simulation	93
protein_sequence	83
protein_protein	77
bioinf_methods	76
protein_evolution	69
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cytoskeleton	44
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myosin	37
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dynein	29
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sequence_comparison	24
eg5	23
ras	23
correlated_mutations	22
nmr	21
motor_model	20
kinases	19
protein_folding	19
domain_motions	18
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docking	16
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correlated_motions	13
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protein_ligand	13
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hbond	11
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general	9
gotit	9
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aaa	8
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small_world	8
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dehydron	7
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guide	3
ion_pairs	3
itc	3
kif1a	3
kin13	3
kin14_kar3	3
membranes	3
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nadp	3
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poster	3
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ptms	1
qm	1
qm_mm	1
rabkinesin	1
rafts	1
ran	1
residue_effect	1
rna	1
rna_dynamics	1
rna_polymerase	1
roc	1
sas	1
scop	1
sequence_conservation	1
sequencing	1
sheer_motion	1
siginal_transduction	1
similarity	1
single_molecule	1
smallrna	1
sos	1
species_evolution	1
structural_genomics	1
structure_alignment	1
superamolecular	1
systems_biology	1
torsion	1
transition_state	1
tyrosine_kinase	1
tyrosine_phosphatases	1
ubiqutin	1
umbrella	1
virulence_factors	1
virus	1
wavelets	1
wham	1
wireing_digrams	1

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