oteri's docking_prog [38 articles] Export

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

	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
	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
	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
	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_prog programmi by oteri on 2009-06-18 15:49:45 as along with 4 people and 1 group robert A_Coletta_Thesis klexa sobolevnrm Structural Biology Group TorVergata
	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
	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
	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
	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
	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
	Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. [My Copy] Journal of computer-aided molecular design, Vol. 21, No. 5. (27 May 2007), pp. 281-306. by A. N. Jain posted to docking docking_prog by oteri on 2009-02-03 17:48:06 as along with 3 people and 3 groups vpenelle BragilMassoud sangeetha Structural Biology Group TorVergata Bioinformatics insilicodrug
	ProPose: a docking engine based on a fully configurable proteinligand interaction model [My Copy] Journal of Molecular Modeling, Vol. 10, No. 5-6. (December 2004), pp. 342-357. by Seifert, Markus, Schmitt, et al. Frank, Herz, Thomas, Kramer, Bernd posted to docking docking_prog by oteri on 2009-01-31 19:06:35 as along with 1 person dgruiz
	Lead Finder: An Approach To Improve Accuracy of Protein-Ligand Docking, Binding Energy Estimation, and Virtual Screening. [My Copy] Journal of chemical information and modeling (13 November 2008) by Oleg V. Stroganov, Fedor N. Novikov, Viktor S. Stroylov, Val Kulkov, Ghermes G. Chilov posted to docking docking_prog by oteri on 2009-01-31 19:00:50 as along with 1 person flbarroso
	Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 20. (1 October 2006), pp. 5856-5868. by Tuan A. Pham, Ajay N. Jain posted to docking docking_prog by oteri on 2009-01-31 18:57:05 as along with 4 people ucbcjbm zfekete schlauchi daevans
	A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 235-249. by E. Perola, W. P. Walters, P. S. Charifson posted to docking docking_prog by oteri on 2009-01-31 18:56:27 as along with 5 people and 3 groups ramensky BragilMassoud yongzhao marcius schlauchi TSRI_MGL BioinfoCIPF SGU-CIPF
	Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. [My Copy] J Med Chem, Vol. 46, No. 4. (13 February 2003), pp. 499-511. by A. N. Jain posted to docking docking_prog by oteri on 2009-01-31 18:54:47 as along with 4 people and 1 group BragilMassoud nachtalp yongzhao schlauchi TSRI_MGL
	[Receptor-ligand docking simulation for membrane proteins] [My Copy] Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan, Vol. 127, No. 1. (January 2007), pp. 123-131. by T. Hirokawa posted to docking docking_prog by oteri on 2009-01-27 23:07:15 as along with 1 group Structural Biology Group TorVergata
	Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Michal Brylinski, Jeffrey Skolnick posted to docking docking_prog by oteri on 2009-01-27 23:06:30 as along with 1 person middledomain
	Protein flexibility in ligand docking and virtual screening to protein kinases. [My Copy] J Mol Biol, Vol. 337, No. 1. (12 March 2004), pp. 209-225. by C. N. Cavasotto, R. A. Abagyan posted to docking docking_prog by oteri on 2009-01-27 13:52:00 as along with 9 people and 3 groups flbarroso BragilMassoud dgruiz yongzhao sangeetha anwazo daevans kazemi LamBras Bioinformatics TSRI_MGL insilicodrug
	FlexE: efficient molecular docking considering protein structure variations [My Copy] Journal of Molecular Biology, Vol. 308, No. 2. (27 April 2001), pp. 377-395. by Holger Clau[ss]en, Christian Buning, Matthias Rarey, Thomas Lengauer posted to docking docking_prog by oteri on 2009-01-27 13:50:23 as along with 5 people and 1 group LamBras apaydin blackbart kazemi carlk Structural Biology Group TorVergata
	ESCAPE 2.0: parallel exhaustive conformational search system of peptides with conformational libraries as building blocks [My Copy] High Performance Computing in the Asia-Pacific Region, 2000. Proceedings. The Fourth International Conference/Exhibition on In High Performance Computing in the Asia-Pacific Region, 2000. Proceedings. The Fourth International Conference/Exhibition on, Vol. 2 (2000), pp. 1097-1102 vol.2. by M. Ando, Y. Akiyama, H. Matsuda posted to analysis_prog docking_prog by oteri on 2009-01-26 09:51:39 as along with 1 group Structural Biology Group TorVergata
	Overview of current docking programs [My Copy] posted to docking_prog by oteri on 2009-01-14 16:41:04 as along with 1 group Structural Biology Group TorVergata
	Biophysical Journal - Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics [My Copy] posted to docking docking_prog by oteri on 2009-01-13 18:18:29 as along with 1 group Structural Biology Group TorVergata
	MADAMM: A multistaged docking with an automated molecular modeling protocol [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 74, No. 1. (2009), pp. 192-206. by Cerqueira, N. F. Bras, P. A. Fernandes, M. J. Ramos posted to docking docking_prog by oteri on 2009-01-13 18:14:16 as
	Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function [My Copy] Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1998), pp. 1639-1662. by Garrett M. Morris, David S. Goodsell, Robert S. Halliday, et al.Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson posted to cepa docking_prog programmi by oteri on 2009-01-12 13:57:27 as along with 23 people and 2 groups trishul nickolay npt11tpn jamalex joule lna Lombardo_7 karinaecomp A_Coletta_Thesis arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain LamBras andreramme UVA_mag_res Chang group TSRI_MGL
	DARWIN: A program for docking flexible molecules [My Copy] Proteins: Structure, Function, and Genetics, Vol. 41, No. 2. (2000), pp. 173-191. by Jeffrey S. Taylor, Roger M. Burnett posted to docking docking_prog by oteri on 2009-01-07 22:56:15 as along with 1 person and 1 group rsood MuraLab
	CONFORMATIONAL TRANSITION PATHWAYS EXPLORED BY MONTE CARLO SIMULATION INTEGRATED WITH COLLECTIVE MODES [My Copy] Biophys. J. (1 August 2008), biophysj.107.128447. by Nigar Kantarci-Carsibasi, Turkan Haliloglu, Pemra Doruker posted to docking_prog by oteri on 2008-12-18 19:38:40 as along with 5 people and 1 group sobolevnrm paulschlesinger viktor21614 sunhwan aqeel baker-group
	DOCK 6.2 User Manual [My Copy] posted to docking_prog user_manual by oteri on 2008-12-10 11:24:54 as along with 1 group Structural Biology Group TorVergata
	Successful Discrimination of Protein Interactions [My Copy] PROTEINS: Structure, Function, and Genetics, Vol. 52 (2003), pp. 92-97. by Carlos J. Camacho, David W. Gatchell posted to docking_prog by oteri on 2008-12-09 10:54:13 as along with 1 group Structural Biology Group TorVergata
	MolDock: A New Technique for High-Accuracy Molecular Docking. [My Copy] J Med Chem, Vol. 49, No. 11. (1 June 2006), pp. 3315-3321. by R. Thomsen, M. H. Christensen posted to docking_prog by oteri on 2008-12-05 10:48:56 as along with 3 people and 1 group rsantana BragilMassoud yongzhao TSRI_MGL
	RosettaLigand Docking with Full Ligand and Receptor Flexibility. [My Copy] Journal of molecular biology (18 November 2008) by Ian W W. Davis, David Baker posted to docking docking_prog by oteri on 2008-12-02 16:05:32 as along with 2 people and 1 group zwang barry McCammon
	MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. [My Copy] European journal of medicinal chemistry (21 October 2008) by Olivier Sperandio, Marc Souaille, François Delfaud, Maria A A. Miteva, Bruno O O. Villoutreix posted to docking_prog by oteri on 2008-12-02 16:04:58 as
	A Flexible Approach to Induced Fit Docking [My Copy] J. Med. Chem. (22 November 2007) by Sander B. Nabuurs, Markus Wagener, Jacob de Vlieg posted to docking docking_prog fleksy by oteri on 2008-12-02 16:03:45 as along with 2 people klexa daevans
	A method to explore transition paths in macromolecules. Applications to hemoglobin and phosphoglycerate kinase [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 263-273. by C. Guilbert posted to docking_prog mordor pedc by oteri on 2008-12-02 15:40:40 as along with 1 person Diego_Prada
	Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets [My Copy] J. Chem. Inf. Model. (30 May 2008) by Christophe Guilbert, Thomas L. James posted to docking_prog mordor by oteri on 2008-12-02 15:37:47 as along with 1 person and 1 group reyez TSRI_MGL
	SODOCK: Swarm optimization for highly flexible protein-ligand docking. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623. by H. M. Chen, B. F. Liu, H. L. Huang, S. F. Hwang, S. Y. Ho posted to docking_prog by oteri on 2008-12-01 17:04:18 as along with 4 people and 1 group npt11tpn BragilMassoud dgruiz yongzhao TSRI_MGL

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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
molecular_dynamics	7
implicit_solvent	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
cuda	1
database	1
electrostatic	1
electrostatics	1
fleksy	1
initial_screening	1
langevin	1
lipid	1
nanocage	1
papvir	1
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protein-protein_docking	1
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rna	1
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oteri's docking_prog [38 articles] Export

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