aqeel's library 387 articles Export

	Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. [My Copy] J Struct Biol, Vol. 125, No. 2-3. (y 1999), pp. 185-195. by W. Wriggers, R. A. Milligan, J. A. McCammon posted to _situs by aqeel on 2009-11-17 22:50:41 as along with 1 person and 2 groups jwm Radiation_Damage Stressosome
	Improved methods for building protein models in electron density maps and the location of errors in these models [My Copy] Acta Crystallographica Section A, Vol. 47, No. 2. (Mar 1991), pp. 110-119. by T. A. Jones, J. Y. Zou, S. W. Cowan, M. Kjeldgaard posted to method_stucturemodel_cryoem by aqeel on 2009-11-11 01:02:35 as
	Molecular Electron Microscopy: State of the Art and Current Challenges [My Copy] ACS Chemical Biology, Vol. 3, No. 5. (1 May 2008), pp. 268-281. by Henning Stahlberg, Thomas Walz posted to review_cryoem by aqeel on 2009-11-04 01:24:29 as along with 1 person zeldin
	The Mechanism and Pathway of pH Induced Swelling in Cowpea Chlorotic Mottle Virus [My Copy] Journal of Molecular Biology, Vol. 318, No. 3. (03 May 2002), pp. 733-747. by Florence Tama, Charles L. Brooks III posted to enm_studies_specific by aqeel on 2009-11-03 17:57:09 as along with 1 person and 1 group ssomani structure-bii
	Flexible Fitting of High-Resolution X-Ray Structures into Cryoelectron Microscopy Maps Using Biased Molecular Dynamics Simulations☆ [My Copy] Biophysical Journal, Vol. 95, No. 12. (15 December 2008), pp. 5692-5705. by Marek Orzechowski, Florence Tama posted to enm_application_cryo-em by aqeel on 2009-10-27 21:32:29 as
	Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps [My Copy] Journal of Structural Biology (02 October 2009) by Ivan Grubisic, Maxim N. Shokhirev, Marek Orzechowski, Osamu Miyashita, Florence Tama posted to enm_application_cryo-em by aqeel on 2009-10-27 21:10:05 as along with 1 person paulschlesinger
	Structure of the E. coli protein-conducting channel bound to a translating ribosome [My Copy] Nature, Vol. 438, No. 7066. (17 November 2005), pp. 318-324. by Kakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, et al.Florence Tama, Simon Jenni, Charles L. Brooks, Nenad Ban, Joachim Frank posted to enm_application_cryo-em_application by aqeel on 2009-10-22 20:01:01 as along with 3 people dayjm ruudvanleeuwen saunders
	Knowledge-Based Real-Space Explorations for Low-Resolution Structure Determination [My Copy] Structure, Vol. 14, No. 8. (August 2006), pp. 1313-1320. by Nicholas Furnham, Andrew S. Dore, Dimitri Y. Chirgadze, Paul I. de Bakker, Mark A. Depristo, Tom L. Blundell posted to ensembles no-printout protein_structure_x-ray by aqeel on 2009-05-23 20:58:29 as along with 1 person TOchi
	Application of a Theory of Enzyme Specificity to Protein Synthesis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 44, No. 2. (February 1958), pp. 98-104. by D. E. Koshland posted to no-tag by aqeel on 2009-05-19 10:34:04 as along with 7 people cen4ik apostola robert kazemi nigham sim82 boris_aguilar
	Einfluss der Configuration auf die Wirkung der Enzyme [My Copy] Berichte der deutschen chemischen Gesellschaft, Vol. 27, No. 3. (1894), pp. 2985-2993. by Emil Fischer posted to lockandkey by aqeel on 2009-05-19 09:58:54 as along with 1 person nigham
	Molecular recognition by induced fit: how fit is the concept? [My Copy] News in physiological sciences : an international journal of physiology produced jointly by the International Union of Physiological Sciences and the American Physiological Society, Vol. 16 (August 2001), pp. 171-173. by H. R. Bosshard posted to dynamics_ligand-induced dynamics_preexisting-equi no-printout by aqeel on 2009-05-18 20:42:08 as
	Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis [My Copy] Angewandte Chemie International Edition, Vol. 38, No. 6. (8 March 1999), pp. 736-749. by Andrew M. Davis, Simon J. Teague posted to dynamics_ligand-induced hydrophobic_effect no-printout by aqeel on 2009-05-18 15:01:13 as along with 3 people lillekatt superpyrin JALumley
	Exploring the common dynamics of homologous proteins. Application to the globin family. [My Copy] Biophys J, Vol. 89, No. 1. (July 2005), pp. 3-13. by S. Maguid, S. Fernandez-Alberti, L. Ferrelli, J. Echave posted to enm_study_evolutionary-deformations no-printout volu by aqeel on 2009-05-01 15:11:01 as along with 5 people and 2 groups gisle barry Einat jlh64 edvin structural_bioinformatics Bioinformatics
	Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351. by B. Qian, A. R. Ortiz, D. Baker posted to enm_study_evolutionary-deformations no-printout by aqeel on 2009-05-01 14:51:36 as along with 5 people and 4 groups ana barry lna marcius dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. [My Copy] Proteins, Vol. 70, No. 1. (1 January 2008), pp. 131-143. by S. Kirillova, J. Cortés, A. Stefaniu, T. Siméon posted to enm_application_pathways by aqeel on 2009-04-28 19:19:42 as
	Prediction of protein conformational freedom from distance constraints. [My Copy] Proteins, Vol. 29, No. 2. (October 1997), pp. 240-251. by B. L. de Groot, D. M. van Aalten, R. M. Scheek, A. Amadei, G. Vriend, H. J. Berendsen posted to dynamics_ensembles_concoord by aqeel on 2009-04-28 19:17:12 as along with 3 people arifor fl simone
	Collective protein dynamics in relation to function [My Copy] Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 165-169. by H. Berendsen posted to no-printout review_ed by aqeel on 2009-04-28 00:01:21 as along with 2 people bmduggan barry
	A refined solution structure of hen lysozyme determined using residual dipolar coupling data. [My Copy] Protein Sci, Vol. 10, No. 4. (April 2001), pp. 677-688. by H. Schwalbe, S. B. Grimshaw, A. Spencer, et al.M. Buck, J. Boyd, C. M. Dobson, C. Redfield, L. J. Smith posted to lysozyme nmr by aqeel on 2009-04-27 01:04:52 as along with 1 person allmensch
	Protein Flexibility and Mobility in Structure-Based Drug Design [My Copy] Front. Drug Des. Discov., Vol. 3 (March 2007), pp. 455-476. by A. Ahmed, S. Kazemi, H. Gohlke posted to review_flexibility-drugdesing by aqeel on 2009-04-20 17:22:31 as along with 2 people and 2 groups fl barry structural_bioinformatics Bioinformatics
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to protein_flexibility_stability by aqeel on 2009-04-19 14:04:53 as along with 10 people and 1 group reyez BragilMassoud dgruiz radestock lna yongzhao choonpeng weisblum higueruelo nickolay TSRI_MGL
	Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis [My Copy] Journal of Molecular Biology, Vol. 274, No. 1. (21 November 1997), pp. 114-131. by J. Ma posted to dynamics_ligand-induced no-printout by aqeel on 2009-04-08 20:44:52 as
	Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: A case study of antibodies [My Copy] BMC Structural Biology, Vol. 7 (17 May 2007), 31. by Ozlem Keskin posted to dynamics_preexisting-equi by aqeel on 2009-04-02 14:57:44 as along with 4 people and 1 group skywalkerus02 sobolevnrm choonpeng medic0747 baker-group
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to dynamics_preexisting-equi by aqeel on 2009-03-26 16:54:37 as along with 8 people and 2 groups oteri bmduggan xdeupi okapi raik ruvido barry zwang structural_bioinformatics McCammon
	Radius of gyration as an indicator of protein structure compactness [My Copy] Molecular Biology, Vol. 42, No. 4. (2008), pp. 623-628. by M. Lobanov, N. Bogatyreva, O. Galzitskaya posted to protein_classes rad_of_gyr by aqeel on 2009-02-25 13:16:38 as
	Iterative cluster-NMA: A tool for generating conformational transitions in proteins. [My Copy] Proteins, Vol. 74, No. 3. (15 February 2009), pp. 760-776. by A. D. Schuyler, R. L. Jernigan, P. K. Qasba, B. Ramakrishnan, G. S. Chirikjian posted to enm_application_pathways by aqeel on 2009-02-07 20:40:16 as along with 1 person and 1 group sobolevnrm baker-group
	Geometry-based sampling of conformational transitions in proteins. [My Copy] Structure (London, England : 1993), Vol. 15, No. 11. (13 November 2007), pp. 1482-1492. by Daniel Seeliger, Jürgen Haas, Bert L. de Groot posted to dynamics_ensembles_concoord by aqeel on 2009-02-07 20:10:38 as along with 2 people arifor cactus
	Rotamer Libraries in the 21st Century [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 4. (1 August 2002), pp. 431-440. by R. Dunbrack posted to review_side-chain rotamer by aqeel on 2009-02-04 16:20:49 as along with 6 people and 5 groups msuarezdiez carlosjavierna apaydin barry joergkurtwegner LamBras structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Modeling side-chain conformation [My Copy] Current Opinion in Structural Biology, Vol. 6, No. 2. (April 1996), pp. 217-221. by M. Vásquez posted to review_side-chain by aqeel on 2009-02-04 16:06:31 as
	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 protein_structure_rotamers by aqeel on 2009-02-03 21:17:36 as along with 3 people carlosjavierna blackbart carlk
	Stereochemical quality of protein structure coordinates [My Copy] Proteins: Structure, Function, and Genetics, Vol. 12, No. 4. (3 February 1992), pp. 345-364. by Anne L. Morris, Malcolm W. Macarthur, E. Gail Hutchinson, Janet M. Thornton posted to procheck ramachandran by aqeel on 2009-02-03 13:41:40 as along with 2 people Diego_Prada andreasauerwein
	Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix. [My Copy] Protein Sci, Vol. 12, No. 11. (November 2003), pp. 2508-2522. by B. K. Ho, A. Thomas, R. Brasseur posted to ramachandran by aqeel on 2009-01-31 20:51:24 as along with 3 people and 1 group Diego_Prada allmensch Einat structural_bioinformatics
	Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms1 [My Copy] Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1711-1733. by Word, Simon C. Lovell, Thomas H. Labean, et al.Hope C. Taylor, Michael E. Zalis, Brent K. Presley, Jane S. Richardson, David C. Richardson posted to protein_structure_validation by aqeel on 2009-01-30 16:17:58 as along with 4 people and 5 groups Diego_Prada dgront barry joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Satisfying hydrogen bonding potential in proteins. [My Copy] J Mol Biol, Vol. 238, No. 5. (20 May 1994), pp. 777-793. by I. K. McDonald, J. M. Thornton posted to protein_structure_hydrobond by aqeel on 2009-01-29 15:21:38 as along with 5 people svozil bicko kaarsinogen lna massivemayhem
	Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds [My Copy] Protein Engineering (May 2002), pp. 359-363. by Ivan Y. Torshin, Irene T. Weber, Robert W. Harrison posted to protein_structure_hydrobond by aqeel on 2009-01-29 15:19:48 as along with 1 person carterb
	Is one solution good enough? [My Copy] Nature Structural & Molecular Biology, Vol. 13, No. 3., pp. 184-185. by Nicholas Furnham, Tom L. Blundell, Mark A. Depristo, Thomas C. Terwilliger posted to protein_structure_validation by aqeel on 2009-01-28 13:26:34 as along with 2 people bicko dgront
	cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. [My Copy] Protein science : a publication of the Protein Society, Vol. 3, No. 2. (February 1994), pp. 176-187. by Madhusudan, E. A. Trafny, N. H. Xuong, et al.J. A. Adams, L. F. Ten Eyck, S. S. Taylor, J. M. Sowadski posted to protein_structure_capk by aqeel on 2009-01-16 16:06:28 as
	Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate [My Copy] Nature, Vol. 370, No. 6490. (1994), pp. 571-575. by Jeanne A. Stuckey, Heidi L. Schubert, Eric B. Fauman, Zhong-Yin Zhang, Jack E. Dixon, Mark A. Saper posted to protein_structure_tyrosine by aqeel on 2009-01-16 15:10:13 as
	Freezing immunoglobulins to see them move. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 17. (27 April 2004), pp. 6466-6471. by L. Bongini, D. Fanelli, F. Piazza, P. De Los Rios, S. Sandin, U. Skoglund posted to antibodies by aqeel on 2009-01-14 17:49:04 as
	Contrasting IgG Structures Reveal Extreme Asymmetry and Flexibility [My Copy] Journal of Molecular Biology, Vol. 319, No. 1. (24 May 2002), pp. 9-18. by E. Saphire, R. Stanfield, M. Maxcrispin, et al.P. Parren, P. Rudd, R. Dwek, D. Burton, I. Wilson posted to antibodies by aqeel on 2009-01-14 17:27:55 as
	Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 252, No. 4. (29 September 1995), pp. 492-503. by P. Hünenberger posted to protein_flexibility_b-factor by aqeel on 2009-01-14 12:52:54 as along with 1 person bmduggan
	Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease. [My Copy] Biophysical journal, Vol. 88, No. 4. (April 2005), pp. 2554-2563. by L. Meinhold, J. C. Smith posted to protein_flexibility_b-factor by aqeel on 2009-01-14 11:55:24 as
	Principles of flexible protein-protein docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 271-289. by Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson posted to review_pro-pro_docking by aqeel on 2008-12-24 13:55:16 as along with 3 people and 1 group bicko csrocha LamBras structural_bioinformatics
	Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility [My Copy] Current Computer - Aided Drug Design, Vol. 4, No. 3. (September 2008), pp. 221-234. by Claudio N. Cavasotto, Narender Singh posted to review_docking by aqeel on 2008-12-24 13:40:16 as
	Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms [My Copy] PLoS Comput Biol, Vol. 4, No. 7. (25 July 2008), e1000135. by Tammy M. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Lio', Tom L. Blundell posted to protein_prediction_snp by aqeel on 2008-12-24 12:58:04 as along with 5 people AbnerCYH aramesh2 GeeSharpMinor aalibes GustavoLacerda
	Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins [My Copy] Biophys. J., Vol. 95, No. 9. (1 November 2008), pp. 4183-4192. by Edward Lyman, Jim Pfaendtner, Gregory A. Voth posted to enm_improvements by aqeel on 2008-12-24 12:46:51 as along with 1 person and 1 group sobolevnrm baker-group
	Target Flexibility: An Emerging Consideration in Drug Discovery and Design. [My Copy] Journal of medicinal chemistry (12 September 2008) by Pietro Cozzini, Glen E. Kellogg, Francesca Spyrakis, et al.Donald J. Abraham, Gabriele Costantino, Andrew Emerson, Francesca Fanelli, Holger Gohlke, Leslie A. Kuhn, Garrett M. Morris, Modesto Orozco, Thelma A. Pertinhez, Menico Rizzi, Christoph A. Sotriffer posted to review_flexibility-drugdesing by aqeel on 2008-12-24 12:38:26 as along with 2 people reyez higueruelo
	Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000129. by M. Cecchini, A. Houdusse, M. Karplus posted to enm_studies_super-mole by aqeel on 2008-12-24 12:27:53 as along with 2 people okapi barry
	A Naturally Occurring Extracellular α−β Clasp Contributes to Stabilization of β3 Integrins in a Bent, Resting Conformation† [My Copy] Biochemistry, Vol. 47, No. 44. (4 November 2008), pp. 11616-11624. by Anthony N. Vomund, Sarah Stuhlsatz-Krouper, Julie Dimitry, Yuhua Song, William A. Frazier posted to integrin by aqeel on 2008-12-24 12:13:24 as along with 1 person choonpeng
	Multiscale methods for macromolecular simulations [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 5. (October 2008), pp. 630-640. by P. Sherwood, B. Brooks, M. Sansom posted to review_coarse-grain by aqeel on 2008-12-24 11:38:52 as along with 6 people and 1 group jonathancooper xavierprat flbarroso carlk choonpeng jmccammon McCammon
	Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations [My Copy] Biophys. J., Vol. 94, No. 5. (1 March 2008), pp. 1613-1621. by Craig C. Jolley, Stephen A. Wells, Petra Fromme, M. F. Thorpe posted to geometric_simulation by aqeel on 2008-12-10 13:53:19 as

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kinase	21
integrin	15
toread	10
enm_studies_specific	8
review_docking	8
dynamics_ensembles_robotic	7
enm_application_pathways	7
enm_improvements_coarse-grain	7
enm_study_evolutionary-deformations	7
md_drug-design	7
no-printout	7
dynamics_ensembles_concoord	6
enm_application_cryo-em	6
enm_studies_comparison	6
enm_studies_super-mole	6
first_study	6
nm_coarse-grained	6
nm_ed	6
protein_structure_validation	6
review_coarse-grain	6
review_flexibility-drugdesing	6
cdk	5
dynamics_preexisting-equi	5
enm_application_md	5
enm_application_struct-refine	5
gnm_studies_specific	5
nm_early-studies	5
protein_flexibility	5
review_enm	5
review_md	5
_bibtex-import	4
dynamics_ensembles_robotic_loop	4
enm	4
enm_studies_early	4
first_application	4
gnm_residue-level	4
gnm_studies_general	4
nma	4
protein_flexibility_b-factor	4
src	4
dynamics_folding	3
dynamics_ligand-induced	3
dynamics_trajectories	3
dynamics_web-db	3
enm_application_docking	3
enm_improvements	3
enm_improvements_connectivity	3
enm_improvements_hessian	3
enm_studies_functional-modes	3
gnm_application	3
hsp90	3
md_coarse-grained	3
md_conf-generation	3
nmr	3
nm_web-db	3
protein_structure_packing	3
protein_structure_side-chains	3
ramachandran	3
review_allostery	3
review_drug-desing	3
review_structure	3
ribosome	3
allostery	2
allostery_example	2
allostery_study	2
antibodies	2
dynamics	2
dynamics_homologous	2
electron_microscopy	2
enm_application_d-enm	2
enm_conformation_morphing	2
first_docking	2
first_theory	2
flex-docking_concoord-ed	2
gnm_improvements	2
gnm_studies_early	2
networks	2
_notavailable	2
protein	2
protein_dataset	2
protein_flexibility_stability	2
protein_structure_hydrobond	2
review_free-energy	2
review_nma	2
review_side-chain	2
tutorial	2
2005_chirikjian	1
2005_moon	1
abc	1
allosteric_potential	1
allostery_dynamic	1
coarse-graining	1
collision_detection	1
distance_constraints	1
dynamcics_trajectories	1
dynamic_pertubation_analysis	1
dynamics_ensembles	1
enm_application_cryo-em_application	1
enm_application_design	1
enm_application_mole-replac	1
enm_coarse-grain_c-nma	1
enm_improvements_combination	1
enm_improvements_morphing	1
enm_improvements_partition	1
enm_studies_cryo-em	1
enm_studies_residue-level	1
ensembles	1
first	1
flex-docking_large-change_loop	1
flex-docking_md	1
flexibility	1
geometric_simulation	1
gnm_web-db	1
helixsheet_transition	1
hiv1	1
hydrophobic_effect	1
industrial_collaboration	1
lockandkey	1
lysozyme	1
md_allostery	1
md_free-energy	1
md_mc	1
mean_field_statsitical_theory	1
method_stucturemodel_cryoem	1
model_go	1
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model_plastic_network	1
modes	1
nm_ed_proteinfolding	1
nm_ed_rmr	1
nm_frequencies	1
nm_studies_general	1
nm_studies_specific	1
normal	1
of	1
procheck	1
protein_classes	1
protein_cracking	1
protein_domain	1
protein_modeling_electrostatic	1
protein_prediction_snp	1
proteinquakes	1
protein_structure_alignment	1
protein_structure_capk	1
protein_structure_modeling	1
protein_structure_prediction	1
protein_structure_rotamers	1
protein_structure_tyrosine	1
protein_structure_x-ray	1
rad_of_gyr	1
rcnma	1
re	1
review_cellstructure	1
review_cryoem	1
review_ed	1
review_pro-pro_docking	1
review_pro-pro-inter	1
review_transition	1
rotamer	1
_situs	1
temp	1
trajectory	1
transporters	1
volu	1

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