Tag protein-ligand_interactions [85 articles] Export

Recent papers classified by the tag protein-ligand_interactions.

	Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure [My Copy] PLoS Comput Biol In PLoS Comput Biol, Vol. 5, No. 12. (4 December 2009), e1000585. by John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser posted to structure protein-ligand_interactions bioinformatics by sobolevnrm on 2009-12-12 00:26:40 as along with 3 people and 1 group hryk apaydin kshameer structural_bioinformatics
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted to protein-ligand_interactions multiscale allostery by sobolevnrm on 2009-10-31 00:13:58 as along with 4 people and 1 group pmung jmccammon agrossfield okapi McCammon
	Computation of conformational coupling in allosteric proteins. [My Copy] PLoS computational biology, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted to structure_prediction protein-ligand_interactions allostery by sobolevnrm on 2009-10-31 00:12:01 as along with 8 people and 1 group apaydin skywalkerus02 klexa oteri boris_aguilar bmduggan barry zwang McCammon
	Theory of Free Energy and Entropy in Noncovalent Binding [My Copy] Chemical Reviews, Vol. 109, No. 9. (9 September 2009), pp. 4092-4107. by Huan-Xiang Zhou, Michael K. Gilson posted to free_energy protein-ligand_interactions review statistical_mechanics by sobolevnrm on 2009-08-10 13:02:10 as along with 7 people and 2 groups jmccammon cchang agrossfield anuragsethi dr_proton qshao paulschlesinger McCammon Chang group
	Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti, Miriam Sgobba posted to electrostatics protein-ligand_interactions solvation by sobolevnrm on 2009-07-23 13:10:49 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Oleg Trott, Arthur J. Olson posted to docking protein-ligand_interactions software by sobolevnrm on 2009-06-18 13:44:04 as along with 4 people and 1 group robert A_Coletta_Thesis klexa oteri Structural Biology Group TorVergata
	Fpocket: An open source platform for ligand pocket detection [My Copy] BMC Bioinformatics, Vol. 10 (02 June 2009), 168. by Vincent Le Guilloux, Peter Schmidtke, Pierre Tuffery posted to bioinformatics protein-ligand_interactions software structure by sobolevnrm on 2009-06-15 00:14:04 as along with 2 people reyez superpyrin
	Inclusion mechanism of steroid drugs into beta-cyclodextrins. Insights from free energy calculations. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 22. (4 June 2009), pp. 7836-7843. by Wensheng Cai, Tingting Sun, Peng Liu, Christophe Chipot, Xueguang Shao posted to free_energy protein-ligand_interactions sterols by sobolevnrm to the group baker-group on 2009-05-11 12:28:12 as along with 1 person liuyz
	Docking for fragment inhibitors of AmpC beta-lactamase. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 18. (5 May 2009), pp. 7455-7460. by D. G. Teotico, K. Babaoglu, G. J. Rocklin, R. S. Ferreira, A. M. Giannetti, B. K. Shoichet posted to docking drug_design protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-05-07 13:00:37 as along with 1 person ubcg08l
	PAPER - Accelerating parallel evaluations of ROCS [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Imran S. Haque, Vijay S. Pande posted to docking programming protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-05-07 13:00:11 as along with 1 person ihaque
	Aminoglycoside Association Pathways with the 30S Ribosomal Subunit [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Maciej Długosz, Joanna Trylska posted to diffusion protein-ligand_interactions ribosome by sobolevnrm to the group baker-group on 2009-04-30 12:16:51 as along with 1 person and 1 group jmccammon McCammon
	AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Garrett M. Morris, Ruth Huey, William Lindstrom, et al.Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson posted to protein-ligand_interactions software by sobolevnrm to the group baker-group on 2009-04-28 12:23:06 as
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted to electrostatics free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-28 12:22:54 as along with 2 people agrossfield flbarroso
	Characterizing the Role of Ensemble Modulation in Mutation-Induced Changes in Binding Affinity [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Anthony Manson, Steven T. Whitten, Josephine C. Ferreon, Robert O. Fox, Vincent J. Hilser posted to allostery protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-04-28 12:22:44 as
	Large-Scale Application of High-Throughput Molecular Mechanics with Poisson-Boltzmann Surface Area for Routine Physics-Based Scoring of Protein-Ligand Complexes. [My Copy] Journal of medicinal chemistry (22 April 2009) by Scott P P. Brown, Steven W W. Muchmore posted to electrostatics free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-24 12:33:50 as
	Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 388, No. 3. (08 May 2009), pp. 644-658. by Anthony Ivetac,, J. n. d. r. e. w. McCammon, posted to enhanced_sampling molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-04-23 12:32:31 as along with 3 people nfparrish bmduggan paulschlesinger
	Applications of computational geometry to the molecular simulation of interfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 046709. by Florencio B. Usabiaga, Daniel Duque posted to geometry protein-ligand_interactions protein-protein_interactions review structure by sobolevnrm to the group baker-group on 2009-04-23 12:30:13 as
	Linear response theory in dihedral angle space for protein structural change upon ligand binding [My Copy] Journal of Computational Chemistry, Vol. 30, No. 16. (2009), pp. 2602-2608. by Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera posted to allostery protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-04-20 12:35:29 as along with 2 people barry RamuAnandakrishnan
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted to bioinformatics protein-ligand_interactions review structure by sobolevnrm to the group baker-group on 2009-04-16 12:35:35 as along with 22 people and 2 groups skywalkerus02 paulymer dfdong tomhebbron anuragsethi ahmetbakan kevinchannon klexa lauresultan dbikard ibuch ramiro2k barry pablocarb ramanuja biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger structural_bioinformatics McCammon
	Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Sheeba J. Irudayam, Richard H. Henchman posted to free_energy protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-04-15 12:11:23 as along with 2 people agrossfield mijam
	Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase, Human Serum Albumin, and Omp32 [My Copy] Journal of Molecular Biology, Vol. 387, No. 4. (10 April 2009), pp. 840-856. by Yifan Song, M. R. Gunner posted to electrostatics pka protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-03-28 16:17:33 as
	Accurate Prediction of Peptide Binding Sites on Protein Surfaces [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (27 March 2009), e1000335. by Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales, Robert B. Russell posted to bioinformatics protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-28 16:16:31 as along with 8 people dfdong higueruelo pablocarb nickolay phoenixzxl neils idoerg paulschlesinger
	Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Devleena Shivakumar, Yuqing Deng, Benoît Roux posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-28 16:14:50 as along with 4 people pachulito carlosjavierna pmk ibuch
	Grand Canonical Free-Energy Calculations of Protein−Ligand Binding [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Matthew Clark, Sia Meshkat, Jeffrey S. Wiseman posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-27 11:57:25 as
	Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for Binding [My Copy] Physical Review Letters, Vol. 102, No. 8. (2009) by Turkan Haliloglu, Burak Erman posted to protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-26 11:36:12 as along with 1 person scratchmandoo
	Path-Integral Method for Predicting Relative Binding Affinities of Protein−Ligand Complexes [My Copy] Journal of the American Chemical Society, Vol. 131, No. 12. (1 April 2009), pp. 4521-4528. by Chandrika Mulakala, Yiannis N. Kaznessis posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-26 11:33:09 as along with 1 person carlosjavierna
	Ligand-induced global transitions in the catalytic domain of protein kinase A [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 9. (3 March 2009), pp. 3023-3028. by Changbong Hyeon, Patricia A. Jennings, Joseph A. Adams, JosÃ© N. Onuchic posted to allostery protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-25 11:32:09 as along with 1 person anwazo
	Computational evaluation of protein-small molecule binding. [My Copy] Current opinion in structural biology, Vol. 19, No. 1. (20 February 2009), pp. 56-61. by O. Guvench, A. D. MacKerell posted to protein-ligand_interactions review by sobolevnrm to the group baker-group on 2009-03-24 12:24:01 as along with 5 people and 1 group flbarroso csrocha ucbcjbm phoenixzxl barry McCammon
	Linking folding and binding [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 1. (February 2009), pp. 31-38. by Peter E. Wright, H. Jane Dyson posted to protein-ligand_interactions protein_folding review by sobolevnrm to the group baker-group on 2009-03-24 12:23:48 as along with 3 people chemrahul82 higueruelo flbarroso
	Ions and Inhibitors in the Binding Site of HIV Protease: Comparison of Monte Carlo Simulations and the Linearized Poisson-Boltzmann Theory [My Copy] Biophysical Journal, Vol. 96, No. 4. (18 February 2009), pp. 1293-1306. by Dezső Boda, Mónika Valiskó, Douglas Henderson, Dirk Gillespie, Bob Eisenberg, Michael K. Gilson posted to electrostatics protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-03-23 11:57:04 as
	Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan posted to protein-ligand_interactions quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-23 11:56:04 as along with 1 person reyez
	Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites [My Copy] BMC Structural Biology, Vol. 8 (27 October 2008), 45. by Andrew T. Binkowski, Andrzej Joachimiak posted to bioinformatics protein-ligand_interactions structure by sobolevnrm to the group baker-group on 2009-03-23 11:52:44 as along with 2 people and 2 groups GeeSharpMinor barry structural_bioinformatics Bioinformatics
	Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns [My Copy] Journal of Molecular Biology, Vol. 387, No. 2. (27 March 2009), pp. 451-464. by Yan Y. Tseng, Joseph Dundas, Jie Liang posted to bioinformatics protein-ligand_interactions structure by sobolevnrm to the group baker-group on 2009-03-23 11:52:33 as along with 3 people and 3 groups pablocarb nickolay barry structural_bioinformatics McCammon Bioinformatics
	Stochastic gating and drug-ribosome interactions. [My Copy] Journal of molecular biology, Vol. 386, No. 3. (27 February 2009), pp. 648-661. by A. C. Vaiana, K. Y. Sanbonmatsu posted to protein-ligand_interactions ribosome by sobolevnrm to the group baker-group on 2009-03-23 11:50:35 as along with 1 person zimbo1
	A Novel Main Chain Motif in Proteins Bridged by Cationic Groups: The Niche☆ [My Copy] Journal of Molecular Biology, Vol. 385, No. 4. (30 January 2009), pp. 1076-1086. by G. Torrance, D. Leader, D. Gilbert, E. Milnerwhite posted to bioinformatics protein-ligand_interactions structure by sobolevnrm to the group baker-group on 2009-03-20 11:50:40 as
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to free_energy molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-18 11:23:06 as along with 9 people and 1 group anuragsethi flbarroso mikaellund barry jmccammon willard agrossfield carlosjavierna ibuch McCammon
	Comparative molecular modeling analysis ofÂ5-amidinoindole and benzamidine binding to thrombin and trypsin: specific H-bond formation contributes to high 5-amidinoindole potency and selectivity for thrombin and factor Xa [My Copy] Journal of Molecular Recognition, Vol. 12, No. 4. (July 1999), pp. 235-241. by Yasheen Zhou, Michael E. Johnson posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:56:37 as
	Energetics of Thrombin−Thrombomodulin Interaction† [My Copy] Biochemistry, Vol. 36, No. 22. (1 June 1997), pp. 6674-6681. by Alessandro Vindigni, Christopher E. White, Elizabeth A. Komives, Enrico Di Cera posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:56:22 as
	MHC-peptide binding is assisted by bound water molecules. [My Copy] J Mol Biol, Vol. 338, No. 2. (23 April 2004), pp. 419-435. by P. M. Petrone, A. E. Garcia posted to protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-03-16 11:56:07 as along with 3 people and 1 group ssomani fjc1 jteyra structure-bii
	Replacement of thrombin residue G184 with Lys or Arg fails to mimic Na<SUP><FONT SIZE='-1'>+</FONT></SUP> binding [My Copy] Proteins: Structure, Function, and Genetics, Vol. 43, No. 3. (2001), pp. 315-318. by Dolly B. Roy, Thierry Rose, Enrico Di Cera posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:55:58 as
	Three-dimensional Modeling of Thrombin-Fibrinogen Interaction [My Copy] J. Biol. Chem., Vol. 277, No. 21. (17 May 2002), pp. 18875-18880. by Thierry Rose, Enrico Di Cera posted to protein-ligand_interactions structure thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:53:59 as
	Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations [My Copy] Journal of Medicinal Chemistry, Vol. 44, No. 7. (1 March 2001), pp. 1043-1050. by Albert C. Pierce, William L. Jorgensen posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:53:34 as
	Structure-based design and synthesis of novel thrombin inhibitors based on phosphinic peptide mimetics [My Copy] Bioorganic & Medicinal Chemistry Letters, Vol. 9, No. 14. (19 July 1999), pp. 1957-1962. by M. Li posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:53:27 as
	Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design. [My Copy] Structure (London, England : 1993), Vol. 4, No. 11. (15 November 1996), pp. 1353-1362. by R. A. Engh, H. Brandstetter, G. Sucher, et al.A. Eichinger, U. Baumann, W. Bode, R. Huber, T. Poll, R. Rudolph, W. von der Saal posted to protein-ligand_interactions thrombin by sobolevnrm to the group baker-group on 2009-03-16 11:52:47 as
	A conserved protonation-dependent switch controls drug binding in the Abl kinase [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 139-144. by Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, et al.Filipp Frank, Huafeng Xu, Morten Jensen, Ron O. Dror, John Kuriyan, David E. Shaw posted to pka protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-05 12:33:56 as along with 2 people nanonan sschurer
	Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral-Equation Theory of Liquids [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 4. (29 January 2009), pp. 873-886. by Norio Yoshida, Takashi Imai, Saree Phongphanphanee, Andriy Kovalenko, Fumio Hirata posted to integral_equation protein-ligand_interactions solvation statistical_mechanics by sobolevnrm to the group baker-group on 2009-03-04 13:10:58 as along with 1 person willard
	Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory [My Copy] Journal of the American Chemical Society, Vol. 131, No. 11. (25 March 2009), pp. 3852-3853. by Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata posted to integral_equation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-03-03 15:58:51 as along with 2 people linkj2 onufriev
	PocketMatch: A new algorithm to compare binding sites in protein structures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 543. by Kalidas Yeturu, Nagasuma Chandra posted to bioinformatics protein-ligand_interactions structure by sobolevnrm to the group baker-group on 2009-03-03 15:52:04 as along with 9 people cdsouthan nanonan pauldobson jteyra kshameer reyez tny higueruelo druvus
	How Electric Fields Modify Alkane Solubility in Lipid Bilayers [My Copy] Science, Vol. 207, No. 4435. (1980), pp. 1075-1077. by Stephen H. White posted to biomembranes electrostatics protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2009-02-28 21:56:49 as
	Direct measurement of protein binding energetics by isothermal titration calorimetry [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 5. (1 September 2001), pp. 560-566. by Stephanie Leavitt, Ernesto Freire posted to experimental_methodology protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-02-28 21:53:03 as along with 2 people barry cactus

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Result page: 1 2 Next

solvation	40
electrostatics	38
bioinformatics	30
structure	24
thrombin	22
free_energy	17
molecular_simulation	16
allostery	12
review	9
drug_design	8
pka	8
quasiharmonic_models	7
statistical_mechanics	7
protein-protein_interactions	6
protein_folding	6
docking	5
integral_equation	5
apbs	4
experimental_methodology	4
protein_engineering	4
quantum_mechanics	4
ribosome	4
software	4
sterols	3
structure_prediction	3
beyond_mean_field	2
biomembranes	2
database	2
diffusion	2
enhanced_sampling	2
geometry	2
metalloregulation	2
molecular_dynamics	2
programming	2
multiscale	1
oxysterols	1
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	1

Tag protein-ligand_interactions [85 articles] Export

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