oteri's docking [146 articles] Export

Recent papers added to oteri's library classified by the tag docking. You can also see everyone's docking.

	A guest molecule–host cavity fitting algorithm to mine PDB for small molecule targets [My Copy] Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1764, No. 8. (August 2006), pp. 1320-1324. by William C. Byrem, Stephen C. Armstead, Shunji Kobayashi, Roderic G. Eckenhoff, David M. Eckmann posted to docking by oteri on 2009-11-01 12:43:24 as
	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2743-2744. by T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, C. Micheletti posted to domain_movement docking by oteri on 2009-10-21 11:44:43 as along with 1 person and 1 group apaydin Structural Biology Group TorVergata
	Synthesis of new modified truncated peptides and inhibition of glycogen phosphorylase. [My Copy] Journal of peptide science : an official publication of the European Peptide Society, Vol. 15, No. 6. (June 2009), pp. 442-450. by Stephanie S. Schweiker, Wendy A. Loughlin, Christopher L. Brown, Gregory K. Pierens posted to peptide docking by oteri on 2009-10-06 16:15:43 as along with 1 group Structural Biology Group TorVergata
	Computation of Conformational Coupling in Allosteric Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted to docking by oteri on 2009-09-27 23:42:36 as along with 6 people and 1 group sobolevnrm klexa boris_aguilar bmduggan barry zwang McCammon
	Molecular dynamic investigation of the interaction of supported affinity ligands with monoclonal antibodies. [My Copy] Biotechnology progress, Vol. 24, No. 3. (n 2008), pp. 527-539. by Laura Zamolo, Valentina Busini, Davide Moiani, Davide Moscatelli, Carlo Cavallotti posted to docking by oteri on 2009-09-27 23:41:04 as
	Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 75, No. 1. (April 2009), pp. 104-110. by Thomas R. Weikl, Carola von Deuster posted to docking by oteri on 2009-09-27 23:38:58 as along with 1 person pablocarb
	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 docking by oteri on 2009-09-27 23:36:05 as along with 8 people and 2 groups bmduggan xdeupi okapi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase. [My Copy] Biophysical journal, Vol. 91, No. 5. (1 September 2006), pp. 1823-1831. by Steven Hayward, Akio Kitao posted to domain_movement docking by oteri on 2009-09-27 23:33:47 as
	Database of ligand-induced domain movements in enzymes. [My Copy] BMC structural biology, Vol. 9 (06 March 2009), 13. by Guoying Qi, Steven Hayward posted to domain_movement docking by oteri on 2009-09-27 23:28:04 as along with 2 people and 1 group sschurer kshameer structural_bioinformatics
	Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A [My Copy] PLoS ONE, Vol. 2, No. 8. (22 August 2007), e761. by Jing Tang, Jewn G. Park, Charles B. Millard, James J. Schmidt, Yuan-Ping Pang posted to znua docking by oteri on 2009-09-17 18:40:07 as along with 2 groups znu Structural Biology Group TorVergata
	Free energy calculations of glycosaminoglycan-protein interactions. [My Copy] Glycobiology, Vol. 19, No. 10. (October 2009), pp. 1103-1115. by Neha S. Gandhi, Ricardo L. Mancera posted to docking by oteri on 2009-09-15 23:17:03 as
	Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 34. (2 September 2009), pp. 12430-12440. by Takashi Imai, Koji Oda, Andriy Kovalenko, Fumio Hirata, Akinori Kidera posted to docking by oteri on 2009-09-15 23:16:31 as along with 1 person somak
	Fragment-based approach to drug lead discovery: overview and advances in various techniques. [My Copy] Drugs in R&D, Vol. 9, No. 4. (2008), pp. 217-227. by Daniela Fattori, Antonella Squarcia, Sandra Bartoli posted to docking by oteri on 2009-09-15 23:16:01 as
	Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation. [My Copy] Proteins, Vol. 66, No. 4. (1 March 2007), pp. 804-813. by Takashi Imai, Ryusuke Hiraoka, Andriy Kovalenko, Fumio Hirata posted to docking by oteri on 2009-09-15 23:15:31 as along with 2 people and 1 group sobolevnrm softsimu baker-group
	Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. [My Copy] Journal of computer-aided molecular design, Vol. 14, No. 6. (August 2000), pp. 559-572. by W. Sippl posted to docking by oteri on 2009-09-15 23:15:05 as
	Computational fragment-based binding site identification by ligand competitive saturation. [My Copy] PLoS computational biology, Vol. 5, No. 7. (10 July 2009), e1000435. by Olgun Guvench, Alexander D. MacKerell posted to docking_prog docking by oteri on 2009-09-15 23:08:22 as along with 5 people and 2 groups NickFurnham higueruelo TRHvidsten barry riffraff structural_bioinformatics McCammon
	Scaffold-hopping potential of fragment-based de novo design: the chances and limits of variation. [My Copy] Combinatorial chemistry & high throughput screening, Vol. 12, No. 4. (May 2009), pp. 383-396. by Bjoern A. Krueger, Axel Dietrich, Karl-Heinz H. Baringhaus, Gisbert Schneider posted to docking by oteri on 2009-09-14 10:46:06 as along with 2 people ubcg08l reyez
	Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. [My Copy] Angewandte Chemie (International ed. in English), Vol. 42, No. 24. (23 June 2003), pp. 2718-2736. by Andrew M. Davis, Simon J. Teague, Gerard J. Kleywegt posted to docking by oteri on 2009-09-14 10:45:23 as along with 3 people and 2 groups apaydin sangeetha thanatos Bioinformatics insilicodrug
	Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design. [My Copy] Journal of chemical information and modeling, Vol. 49, No. 5. (May 2009), pp. 1211-1222. by Britta Nisius, Ulrich Rester posted to docking by oteri on 2009-09-14 10:45:13 as along with 2 people reyez sschurer
	DOCK 6: combining techniques to model RNA-small molecule complexes. [My Copy] RNA (New York, N.Y.), Vol. 15, No. 6. (15 June 2009), pp. 1219-1230. by P. Therese Lang, Scott R. Brozell, Sudipto Mukherjee, et al.Eric F. Pettersen, Elaine C. Meng, Veena Thomas, Robert C. Rizzo, David A. Case, Thomas L. James, Irwin D. Kuntz posted to docking_prog docking by oteri on 2009-09-14 10:44:30 as along with 1 person simone
	Study on the inhibitory mechanism and binding mode of the hydroxycoumarin compound NSC158393 to HIV-1 integrase by molecular modeling. [My Copy] Biopolymers, Vol. 91, No. 9. (September 2009), pp. 700-709. by Ming Liu, Xiao Jing J. Cong, Ping Li, Jian Jun J. Tan, Wei Zu Z. Chen, Cun Xin X. Wang posted to docking by oteri on 2009-09-14 10:43:56 as along with 1 person carlosjavierna
	E-novo: an automated workflow for efficient structure-based lead optimization. [My Copy] Journal of chemical information and modeling, Vol. 49, No. 7. (24 July 2009), pp. 1797-1809. by Bradley C. Pearce, David R. Langley, Jia Kang, Hongwei Huang, Amit Kulkarni posted to docking_prog docking by oteri on 2009-09-14 10:43:33 as along with 1 person superpyrin
	Multiscale generalized born modeling of ligand binding energies for virtual database screening. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 35. (3 September 2009), pp. 11793-11799. by Hao-Yang Y. Liu, Sam Z. Grinter, Xiaoqin Zou posted to docking by oteri on 2009-09-14 10:40:45 as
	Automated site preparation in physics-based rescoring of receptor ligand complexes. [My Copy] Proteins, Vol. 77, No. 1. (October 2009), pp. 52-61. by Chaya S. Rapp, Cheryl Schonbrun, Matthew P. Jacobson, Chakrapani Kalyanaraman, Niu Huang posted to docking by oteri on 2009-09-14 10:40:34 as along with 3 people and 1 group klexa jmccammon RamuAnandakrishnan McCammon
	Importance of Ligand Reorganization Free Energy in Protein-Ligand Binding-Affinity Prediction. [My Copy] Journal of the American Chemical Society (8 September 2009) by Chao-Yie Y. Yang, Haiying Sun, Jianyong Chen, Zaneta Nikolovska-Coleska, Shaomeng Wang posted to implicit_solvent docking by oteri on 2009-09-14 10:40:23 as
	Generalized born models of macromolecular solvation effects. [My Copy] Annual review of physical chemistry, Vol. 51, No. 1. (2000), pp. 129-152. by D. Bashford, D. A. Case posted to implicit_solvent docking by oteri on 2009-09-14 10:40:08 as along with 4 people ras flbarroso dgront RamuAnandakrishnan
	Improving implicit solvent simulations: a Poisson-centric view. [My Copy] Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 137-143. by Nathan A. Baker posted to implicit_solvent docking by oteri on 2009-09-14 10:39:56 as along with 5 people flbarroso softsimu ttjoseph qwermish RamuAnandakrishnan
	Integrated Modeling Program, Applied Chemical Theory (IMPACT). [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1752-1780. by Jay L. Banks, Hege S. Beard, Yixiang Cao, et al.Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy posted to docking by oteri on 2009-09-14 10:39:28 as along with 2 people flbarroso onufriev
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted to docking by oteri on 2009-09-14 10:39:15 as along with 7 people r2s2 flbarroso LamBras BragilMassoud qwermish RamuAnandakrishnan jteyra
	Normal-mode-analysis-monitored energy minimization procedure for generating small-molecule bound conformations. [My Copy] PloS one, Vol. 2, No. 10. (2007) by Qi Wang, Yuan-Ping P. Pang posted to docking by oteri on 2009-09-02 16:11:49 as
	A protein-DNA docking benchmark [My Copy] Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), e88. by Marc van Dijk, Alexandre M. Bonvin posted to dna docking by oteri on 2009-06-06 21:44:09 as along with 4 people HawkinsJohnC reyez neils boris_aguilar
	Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility [My Copy] Nucl. Acids Res., Vol. 34, No. 11. (4 July 2006), pp. 3317-3325. by Marc van Dijk, Aalt D. van Dijk, Victor Hsu, Rolf Boelens, Alexandre M. Bonvin posted to dna docking docking_prog by oteri on 2009-06-06 21:42:02 as along with 1 person HawkinsJohnC
	Vibrational Dynamics of Icosahedrally Symmetric Biomolecular Assemblies Compared with Predictions Based on Continuum Elasticity [My Copy] Biophysical Journal, Vol. 96, No. 11. (03 June 2009), pp. 4438-4448. by Zheng Yang, Ivet Bahar, Michael Widom posted to docking by oteri on 2009-06-06 15:33:20 as
	Mining Molecular Fragments: Finding Relevant Substructures of Molecules [My Copy] posted to docking by oteri on 2009-04-13 14:41:35 as along with 1 person and 1 group klexa Structural Biology Group TorVergata
	Flexible protein alignment and hinge detection. [My Copy] Proteins, Vol. 48, No. 2. (1 August 2002), pp. 242-256. by Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson posted to docking by oteri on 2009-04-03 17:24:39 as along with 2 people ubcg08l nickolay
	ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by Meytal Landau, Itay Mayrose, Yossi Rosenberg, et al.Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal posted to docking docking_prog by oteri on 2009-04-03 17:06:29 as along with 8 people and 1 group pablocarb tomjad klexa shacko ramiro2k chrn sriram_s bicko Structural Biology Group TorVergata
	ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 163-164. by F. Glaser, T. Pupko, I. Paz, et al.R. E. Bell, D. Bechor-Shental, E. Martz, N. Ben-Tal posted to docking docking_prog by oteri on 2009-04-03 17:05:47 as along with 4 people and 1 group tomjad chrn bicko siebertm Structural Biology Group TorVergata
	Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences. [My Copy] J Steroid Biochem Mol Biol, Vol. 103, No. 3-5. (March 2007), pp. 357-360. by M. Kurcinski, A. Kolinski posted to docking by oteri on 2009-04-03 16:45:47 as along with 2 people and 1 group klexa mkurc Structural Biology Group TorVergata
	AutoGrow: a novel algorithm for protein inhibitor design. [My Copy] Chemical biology & drug design, Vol. 73, No. 2. (February 2009), pp. 168-178. by Jacob D. Durrant, Rommie E. Amaro, J. Andrew McCammon posted to docking by oteri on 2009-03-15 22:48:27 as along with 1 person and 2 groups klexa Structural Biology Group TorVergata LOX-1 Receptor
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to docking by oteri on 2009-02-16 16:38:49 as along with 5 people and 2 groups pansapiens klexa abovell sobolevnrm middledomain baker-group Structural Biology Group TorVergata
	Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites [My Copy] Journal of Molecular Modeling by Alexander Berchanski, Aviva Lapidot posted to docking by oteri on 2009-02-13 14:06:54 as
	Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin [My Copy] Proteins: Structure, Function, and Genetics, Vol. 40, No. 2. (2000), pp. 258-289. by Collin M. Stultz, Martin Karplus posted to docking docking_prog by oteri on 2009-02-13 14:05:32 as along with 1 group Structural Biology Group TorVergata
	An automated method for dynamic ligand design. [My Copy] Proteins, Vol. 23, No. 4. (December 1995), pp. 472-490. by A. Miranker, M. Karplus posted to docking docking_prog by oteri on 2009-02-13 14:05:14 as along with 2 people and 1 group klexa dfgreen Structural Biology Group TorVergata
	FlexNovo: Structure-Based Searching in Large Fragment Spaces [My Copy] posted to docking docking_prog by oteri on 2009-02-13 14:04:51 as along with 1 person and 1 group klexa Structural Biology Group TorVergata
	Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking [My Copy] posted to docking by oteri on 2009-02-04 18:07:50 as
	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1549-1562. by Guosheng Wu, Daniel H. Robertson, Charles L. Brooks, Michal Vieth posted to docking docking_prog by oteri on 2009-02-03 18:02:34 as along with 5 people and 1 group oceanwind apostola papatonyhill mmuecke msuarezdiez Structural Biology Group TorVergata
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted to docking by oteri on 2009-02-03 18:01:44 as along with 25 people and 4 groups rabio ucbcjbm flbarroso csrocha timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Structural Biology Group TorVergata Bioinformatics TSRI_MGL insilicodrug
	A review of protein-small molecule docking methods. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted to docking by oteri on 2009-02-03 17:58:47 as along with 6 people and 5 groups klexa csrocha marcius sangeetha schlauchi massivemayhem Structural Biology Group TorVergata Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Automated docking and the search for HIV protease inhibitors. [My Copy] SAR QSAR Environ Res, Vol. 8, No. 3-4. (1998), pp. 273-285. by A. J. Olson, D. S. Goodsell posted to docking drug_design qsar by oteri on 2009-02-03 17:58:13 as along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
	Comparative evaluation of eight docking tools for docking and virtual screening accuracy. [My Copy] Proteins, Vol. 57, No. 2. (1 November 2004), pp. 225-242. by E. Kellenberger, J. Rodrigo, P. Muller, D. Rognan posted to docking docking_prog by oteri on 2009-02-03 17:52:55 as along with 5 people and 2 groups klexa BragilMassoud dgruiz sangeetha schlauchi Bioinformatics insilicodrug

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docking	146
lox-1	75
dna	46
coiled_coil	40
docking_prog	38
cepa	32
programmi	24
drug_design	20
dna_nanostructures	19
neck_domain	16
topo	15
cluster_analysis	12
figata	11
adducts	8
algorithm	8
implicit_solvent	6
molecular_dynamics	6
znua	5
methods	4
protein-peptide_dock	4
structure_prediction	4
circular_dichroism	3
cpt	3
domain_movement	3
ambertools	2
artificial_intelligence	2
chiancone	2
coarse_grained	2
guidelines	2
inibitori	2
modelling	2
mordor	2
namd	2
nmr_and_md	2
peptide	2
protein-protein_dock	2
ricerche	2
user_manual	2
analysis_prog	1
carrier	1
database	1
electrostatic	1
electrostatics	1
fleksy	1
initial_screening	1
langevin	1
lipid	1
nanocage	1
papvir	1
pedc	1
protein-protein_docking	1
qsar	1
rna	1
server	1

oteri's docking [146 articles] Export

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