Andrea Coletta's Top Recommendations

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	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted by 10 people RamuAnandakrishnan mikaellund Structural Biology Group TorVergata oteri nickolay flbarroso choonpeng sobolevnrm baker-group onufriev
	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 by 30 people rabio ucbcjbm flbarroso csrocha Structural Biology Group TorVergata oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Bioinformatics TSRI_MGL insilicodrug Evangelia nigham
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted by 13 people anuragsethi Diego_Prada scampos Structural Biology Group TorVergata oteri barry daevans sobolevnrm structural_bioinformatics baker-group LamBras allmensch GermanErlenkamp
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted by 19 people mijogiffin Chang group flbarroso GermanErlenkamp onufriev arlam Structural Biology Group TorVergata oteri McCammon jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi
	Replica-exchange molecular dynamics method for protein folding [My Copy] Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151. by Y. Sugita posted by 10 people chemrahul82 tovrstra Diego_Prada Structural Biology Group TorVergata oteri Sylvain_Prigent andreasauerwein dgront allmensch rulix
	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 by 8 people pansapiens klexa abovell baker-group sobolevnrm Structural Biology Group TorVergata oteri middledomain
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted by 7 people anuragsethi klexa tovrstra Structural Biology Group TorVergata oteri onufriev softsimu
	Biopython: freely available Python tools for computational molecular biology and bioinformatics [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1422-1423. by Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, et al.Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon posted by 47 people Geknitics pekrau Systems_Biology Computational_Systems_Biology Sergey_gerbek hwright jfr karinaecomp applebyb klexa rdiaz FabienneGranier thegoose Structural Biology Group TorVergata oteri cmzmasek jwm guhjy Journal picks AlexBateman daforerog ltitodem Thaverkamp baker-group sobolevnrm psique Bioinformatics dswan neils dullhunk bertelsen Vincent_Rouilly gwallau brianb jorisslob svenrahmann jmeppley VGreiff sjcockell druvus Software-Architecture OER_Open_Educational_Resources Method_Engineering_Services jago kshameer operon svozil
	Molecular simulations of lipid mediated protein-protein interactions [My Copy] Biophys. J. (16 May 2008), biophysj.107.124164. by Frederick J. de Meyer, Maddalena Venturoli, Berend Smit posted by 5 people Structural Biology Group TorVergata oteri choonpeng paulschlesinger agrossfield
	PDB file parser and structure class implemented in Python [My Copy] Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2308-2310. by Thomas Hamelryck, Bernard Manderick posted by 9 people edws klexa Structural Biology Group TorVergata oteri dgruiz bicko dgront rabio massivemayhem
	Assessing equilibration and convergence in biomolecular simulations. [My Copy] Proteins, Vol. 48, No. 3. (15 August 2002), pp. 487-496. by Lorna J. Smith, Xavier Daura, Wilfred F. van Gunsteren posted by 6 people bmduggan baker-group sobolevnrm Structural Biology Group TorVergata oteri mleis
	Bridging from molecular simulation to biochemical networks. [My Copy] Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 166-172. by M. Stein, R. R. Gabdoulline, R. C. Wade posted by 11 people anuragsethi choonpeng Structural Biology Group TorVergata oteri ocs aqeel Borelli cmmorel julius ras higueruelo
	Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics [My Copy] Biophys. J. (26 September 2008), biophysj.108.131649. by Cyril Azuara, Henri Orland, Michael Bon, Patrice Koehl, Marc Delarue posted by 6 people baker-group sobolevnrm Structural Biology Group TorVergata oteri onufriev Elena_Zubova
	Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 2. (9 November 2007), pp. 399-421. by Sheng-You Huang, Xiaoqin Zou posted by 11 people nickolay Structural Biology Group TorVergata oteri AliceWang BragilMassoud bicko yongzhao kazemi hmk TSRI_MGL LamBras
	De novo design of the hydrophobic cores of proteins. [My Copy] Protein Sci, Vol. 4, No. 10. (October 1995), pp. 2006-2018. by J. R. Desjarlais, T. M. Handel posted by 5 people Structural Biology Group TorVergata oteri dfgreen ashaytan chgjb
	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. [My Copy] J Comput Aided Mol Des (15 January 2008) by Rommie E. Amaro, Riccardo Baron, J A. McCammon posted by 9 people karinaecomp Structural Biology Group TorVergata oteri McCammon jmccammon rbaron higueruelo kazemi LamBras
	HOLE: a program for the analysis of the pore dimensions of ion channel structural models. [My Copy] Journal of molecular graphics, Vol. 14, No. 6. (December 1996) by O. S. Smart, J. G. Neduvelil, X. Wang, B. A. Wallace, M. S. Sansom posted by 6 people dimka Structural Biology Group TorVergata oteri jwm Radiation_Damage Stressosome
	Open source clustering software. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 9. (12 June 2004), pp. 1453-1454. by M. J. de Hoon, S. Imoto, J. Nolan, S. Miyano posted by 33 people dakelley rabio klexa Structural Biology Group TorVergata oteri arlam ilyashl matterhorn cswinburne mtagaya macowell davidbroadhurst eme oilcan rahul Ayest balajis piscinero metamerist digisoki wnpx rafamayo atopcu ccr calu Fluid-Mechanics-and-Thermal-Science-Research astro SRL Computational_Systems_Biology XMLDataManagement BUiGEM karlmicha chad_davis
	Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 27. (1 July 2008), pp. 8188-8197. by Daniel Svozil, Judit E. Šponer, Ivan Marchan, et al.Alberto Pérez, Thomas E. Cheatham, F. Forti, F. Javier Luque, Modesto Orozco, Jiří Šponer posted by 3 people Structural Biology Group TorVergata oteri middledomain
	NMR and molecular dynamics studies of the interaction of melatonin with calmodulin [My Copy] Protein Science, Vol. 13, No. 11. (1 November 2004), pp. 2925-2938. by Adrián G. Turjanski, Darío A. Estrin, Ruth E. Rosenstein, et al.John E. Mccormick, Stephen R. Martin, Annalisa Pastore, Rodolfo R. Biekofsky, Vincenzo Martorana posted by 4 people flbarroso Structural Biology Group TorVergata oteri mkrishna
	Molecular modeling of hydration in drug design. [My Copy] Current opinion in drug discovery & development, Vol. 10, No. 3. (May 2007), pp. 275-280. by R. L. Mancera posted by 4 people flbarroso Structural Biology Group TorVergata oteri superpyrin
	Biomolecular simulation and modelling: status, progress and prospects. [My Copy] Journal of the Royal Society, Interface / the Royal Society, Vol. 5 Suppl 3, No. 0. (6 December 2008), pp. S173-S190. by Marc W. van der Kamp, Katherine E. Shaw, Christopher J. Woods, Adrian J. Mulholland posted by 4 people Structural Biology Group TorVergata oteri McCammon jmccammon
	Recent progress and future directions in protein-protein docking. [My Copy] Current protein & peptide science, Vol. 9, No. 1. (February 2008), pp. 1-15. by D. W. Ritchie posted by 3 people flbarroso Structural Biology Group TorVergata oteri
	Physics-based methods for studying protein-ligand interactions. [My Copy] Curr Opin Drug Discov Devel, Vol. 10, No. 3. (May 2007), pp. 325-331. by N. Huang, M. P. Jacobson posted by 5 people flbarroso Structural Biology Group TorVergata oteri superpyrin higueruelo
	Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (15 November 2001), pp. 34-40. by Fredrik österberg, Garrett M. Morris, Michel F. Sanner, Arthur J. Olson, David S. Goodsell posted by 5 people Structural Biology Group TorVergata oteri yongzhao peprovy TSRI_MGL
	QXP: powerful, rapid computer algorithms for structure-based drug design. [My Copy] J Comput Aided Mol Des, Vol. 11, No. 4. (July 1997), pp. 333-344. by C. McMartin, R. S. Bohacek posted by 4 people flbarroso Structural Biology Group TorVergata oteri BragilMassoud
	Efficient docking of peptides to proteins without prior knowledge of the binding site. [My Copy] Protein science : a publication of the Protein Society. , Vol. 11, No. 7. (July 2002), pp. 1729-1737. by Csaba Hetényi, David van der Spoel posted by 6 people npt11tpn Structural Biology Group TorVergata oteri yongzhao TSRI_MGL rguenther
	Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure. [My Copy] Journal of structural biology, Vol. 163, No. 3. (8 September 2008), pp. 258-269. by David A. Parry, Bruce D. Fraser, John M. Squire posted by 7 people martainn Lombardo_7 Structural Biology Group TorVergata LOX-1 Receptor oteri kevinchannon kgutwin
	Assessment of standard force field models against high-quality <I>ab initio</I> potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2187-2193. by C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, et al.Michael S. Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould posted by 3 people Structural Biology Group TorVergata oteri RamuAnandakrishnan
	FE: 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 by 7 people LamBras Structural Biology Group TorVergata oteri apaydin blackbart kazemi carlk
	Guided Docking Approaches to Structure-Based Design and Screening [My Copy] Current Topics in Medicinal Chemistry, Vol. 4, No. 7. (March 2004), pp. 687-700. by X. Fradera, J. Mestres posted by 7 people Structural Biology Group TorVergata oteri LamBras dgruiz sangeetha Bioinformatics insilicodrug
	DNA basepair step deformability inferred from molecular dynamics simulations. [My Copy] Biophysical journal, Vol. 85, No. 5. (1 November 2003), pp. 2872-2883. by Filip Lankas, Jirí Sponer, Jörg Langowski, Thomas E. Cheatham posted by 5 people Structural Biology Group TorVergata oteri Elena_Zubova ruvido onufriev
	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 by 10 people pablocarb tomjad klexa shacko Structural Biology Group TorVergata oteri ramiro2k chrn sriram_s bicko
	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 by 4 people klexa Structural Biology Group TorVergata oteri dfgreen
	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 by 12 people klexa csrocha Structural Biology Group TorVergata oteri marcius sangeetha schlauchi massivemayhem Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Searching Fragment Spaces with Feature Trees [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Uta Lessel, Bernd Wellenzohn, Markus Lilienthal, Holger Claussen posted by 4 people zimbo1 reyez Structural Biology Group TorVergata oteri
	Algorithms for computing the volume and other integral properties of solids. II. A family of algorithms based on representation conversion and cellular approximation [My Copy] Commun. ACM, Vol. 25, No. 9. (1982), pp. 642-650. by Yong T. Lee, Aristides A. G. Requicha posted by 3 people RamuAnandakrishnan Structural Biology Group TorVergata oteri
	A semiempirical free energy force field with charge-based desolvation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (1 February 2007), pp. 1145-1152. by Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell posted by 7 people nickolay joule Structural Biology Group TorVergata oteri IrinaMoreira BragilMassoud carlescorbi
	The pore dimensions of gramicidin A. [My Copy] Biophys J, Vol. 65, No. 6. (December 1993), pp. 2455-2460. by O. S. Smart, J. M. Goodfellow, B. A. Wallace posted by 5 people Structural Biology Group TorVergata oteri jwm Radiation_Damage Stressosome
	Modification of the CHARMM force field for DMPC lipid bilayer [My Copy] Journal of Computational Chemistry, Vol. 29, No. 14. (2008), pp. 2359-2369. by Carl-Johan Högberg, Alexei M. Nikitin, Alexander P. Lyubartsev posted by 4 people Structural Biology Group TorVergata LOX-1 Receptor oteri agrossfield
	Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. [My Copy] Proteins, Vol. 60, No. 2. (1 August 2005), pp. 245-251. by C. J. Camacho posted by 4 people Structural Biology Group TorVergata oteri qzhang TSRI_MGL
	De Novo Drug Design Using Multiobjective Evolutionary Graphs [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Christos A. Nicolaou, Joannis Apostolakis, Costas S. Pattichis posted by 4 people sschurer carlosjavierna Structural Biology Group TorVergata oteri
	SPICKER: a clustering approach to identify near-native protein folds. [My Copy] J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 865-871. by Y. Zhang, J. Skolnick posted by 6 people klexa Structural Biology Group TorVergata oteri j3xucite iakes nigham
	Do rotamer libraries reproduce the side-chain conformations of peptidic ligands from the PDB? [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 5. (17 January 2009), pp. 611-619. by A. Pupo, E. Moreno posted by 4 people carlosjavierna sschurer Structural Biology Group TorVergata oteri
	Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? [My Copy] BMC Bioinformatics, Vol. 9 (07 January 2008), 6. by Jean-Francois Taly, Antoine Marin, Jean-Francois Gibrat posted by 4 people Structural Biology Group TorVergata oteri biehl LamBras
	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 by 7 people vpenelle Structural Biology Group TorVergata oteri BragilMassoud sangeetha Bioinformatics insilicodrug
	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 by 4 people klexa Structural Biology Group TorVergata oteri mkurc
	Evaluating Docking Methods for Prediction of Binding Affinities of Small Molecules to the G Protein βγ Subunits [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Min-Sun Park, Axel L. Dessal, Alan V. Smrcka, Harry A. Stern posted by 3 people carlosjavierna Structural Biology Group TorVergata oteri
	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 by 4 people klexa Structural Biology Group TorVergata LOX-1 Receptor oteri
	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 by 7 people oceanwind Structural Biology Group TorVergata oteri apostola papatonyhill mmuecke msuarezdiez
	Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments [My Copy] In Annual Reports in Computational Chemistry Volume 5, Vol. 5 (2009), pp. 79-98. by Danny Perez, Blas P. Uberuaga, Yunsic Shim, Jacques G. Amar, Arthur F. Voter posted by 3 people anuragsethi Structural Biology Group TorVergata oteri
	A short guide for molecular dynamics simulations of RNA systems [My Copy] Methods, Vol. 47, No. 3. (March 2009), pp. 187-197. by Yaser Hashem, Pascal Auffinger posted by 3 people itolokh Structural Biology Group TorVergata oteri
	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 by 6 people tomjad Structural Biology Group TorVergata oteri chrn bicko siebertm
	Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Sebastian G. Rohrer, Knut Baumann posted by 3 people sschurer Structural Biology Group TorVergata oteri
	Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction [My Copy] J. Am. Chem. Soc., Vol. 118, No. 26. (3 July 1996), pp. 6131-6140. by X. Li, X. Yang, J. Qi, N. C. Seeman posted by 3 people Structural Biology Group TorVergata oteri dna
	alpha/gamma Transitions in the B-DNA backbone [My Copy] Nucl. Acids Res., Vol. 30, No. 24. (15 December 2002), pp. 5398-5406. by Peter Varnai, Dragana Djuranovic, Richard Lavery, Brigitte Hartmann posted by 3 people Structural Biology Group TorVergata oteri Elena_Zubova
	Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins [My Copy] IEEE Trans. Parallel Distrib. Syst., Vol. 13, No. 6. (2002), pp. 544-555. by Natsuhiki Futamura, Srinivas Aluru, Desh Ranjan, Bhanu Hariharan posted by 4 people Structural Biology Group TorVergata LOX-1 Receptor oteri mijam
	Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles [My Copy] Structure, Vol. 14, No. 10. (October 2006), pp. 1527-1534. by Filip Lankas, Richard Lavery, John H. Maddocks posted by 3 people Structural Biology Group TorVergata oteri onufriev
	iMembrane: Homology-Based Membrane-Insertion of Proteins. [My Copy] Bioinformatics (Oxford, England) (23 February 2009) by Sebastian Kelm, Jiye Shi, Charlotte M M. Deane posted by 5 people OPIG sebk friendpine Structural Biology Group TorVergata oteri
	Rational design of affinity peptide ligand by flexible docking simulation [My Copy] Journal of Chromatography A, Vol. 1146, No. 1. (30 March 2007), pp. 41-50. by Fu-Feng Liu, Tao Wang, Xiao-Yan Dong, Yan Sun posted by 3 people Structural Biology Group TorVergata oteri carlescorbi
	Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. [My Copy] Nucleic acids research, Vol. 36, No. 1. (5 January 2008), pp. 21-29. by Sarah A. Harris, Charles A. Laughton, Tanniemola B. Liverpool posted by 2 people Structural Biology Group TorVergata oteri
	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 by 2 people Structural Biology Group TorVergata oteri
	Open-architecture Implementation of Fragment Molecular Orbital Method for Peta-scale Computing [My Copy] (11 Jan 2007) by Toshiya Takami, Jun Maki, Jun-Ichi Ooba, et al.Yuichi Inadomi, Hiroaki Honda, Taizo Kobayashi, Rie Nogita, Mutsumi Aoyagi posted by 2 people Structural Biology Group TorVergata oteri
	Comparison of analyses of DNA curvature. [My Copy] Journal of biomolecular structure & dynamics, Vol. 21, No. 1. (August 2003), pp. 89-97. by A. Barbic, D. M. Crothers posted by 2 people Structural Biology Group TorVergata oteri
	Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. [My Copy] Biopolymers, Vol. 73, No. 3. (15 February 2004), pp. 380-403. by D. L. Beveridge, S. B. Dixit, G. Barreiro, K. M. Thayer posted by 2 people Structural Biology Group TorVergata oteri
	DNA bending: the prevalence of kinkiness and the virtues of normality. [My Copy] Nucleic acids research, Vol. 26, No. 8. (15 April 1998), pp. 1906-1926. by R. E. Dickerson posted by 2 people Structural Biology Group TorVergata oteri
	Defining the structure of irregular nucleic acids: conventions and principles. [My Copy] Journal of biomolecular structure & dynamics, Vol. 6, No. 4. (February 1989), pp. 655-667. by R. Lavery, H. Sklenar posted by 2 people Structural Biology Group TorVergata oteri
	Recent Progress and Future Directions in Protein-Protein Docking [My Copy] Current Protein and Peptide Science, Vol. 9, No. 1. (February 2008), pp. 1-15. by Ritchie, W. David posted by 5 people HawkinsJohnC Structural Biology Group TorVergata oteri TobiasAbenius timg
	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 by 2 people Structural Biology Group TorVergata oteri
	Discovery of Potent Thermolysin Inhibitors Using Structure Based Virtual Screening and Binding Assays [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 1. (January 2009), pp. 48-61. by Mahmud T. Khan, Ole-Martin Fuskevåg, Ingebrigt Sylte posted by 3 people Structural Biology Group TorVergata LOX-1 Receptor oteri
	Docking Studies on a New Human Immodeficiency Virus Integrase−Mg−DNA Complex: Phenyl Ring Exploration and Synthesis of 1H-Benzylindole Derivatives through Fluorine Substitutions [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 2. (22 January 2009), pp. 569-573. by Stefania Ferro, Laura De Luca, Maria L. Barreca, et al.Nunzio Iraci, Sara De Grazia, Frauke Christ, Myriam Witvrouw, Zeger Debyser, Alba Chimirri posted by 2 people Structural Biology Group TorVergata oteri
	Characterization of the papillomavirus α1E2 peptide unfolded to folded transition upon DNA binding [My Copy] FEBS Letters, Vol. 582, No. 25-26. (29 October 2008), pp. 3619-3624. by G. Giesel, L. Lima, J. Faberbarata, J. Guimaraes, H. Verli posted by 2 people Structural Biology Group TorVergata oteri
	Conformational analysis of nucleic acids revisited: Curves+ [My Copy] Nucl. Acids Res. (22 July 2009), gkp608. by R. Lavery, M. Moakher, J. H. Maddocks, D. Petkeviciute, K. Zakrzewska posted by 2 people Structural Biology Group TorVergata oteri
	Supercoiling and denaturation of DNA loops. [My Copy] Physical review letters, Vol. 100, No. 23. (13 June 2008) by T. B. Liverpool, S. A. Harris, C. A. Laughton posted by 2 people Structural Biology Group TorVergata oteri
	ProtNet: a tool for stochastic simulations of protein interaction networks dynamics [My Copy] BMC Bioinformatics, Vol. 8, No. Suppl 1. (2007) by Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni posted by 3 people Structural Biology Group TorVergata oteri ullahmukhtar
	Inhibitory effect of conjugated eicosapentaenoic acid on human DNA topoisomerases I and II. [My Copy] Archives of biochemistry and biophysics, Vol. 435, No. 1. (1 March 2005), pp. 197-206. by Y. Yonezawa, T. Tsuzuki, T. Eitsuka, et al.T. Miyazawa, T. Hada, K. Uryu, C. Murakami-Nakai, H. Ikawa, I. Kuriyama, M. Takemura, M. Oshige, H. Yoshida, K. Sakaguchi, Y. Mizushina posted by 2 people Structural Biology Group TorVergata oteri
	Crystal structure of a conserved N-terminal domain of histone deacetylase 4 reveals functional insights into glutamine-rich domains [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 11. (13 March 2007), pp. 4297-4302. by Liang Guo, Aidong Han, Darren L. Bates, Jue Cao, Lin Chen posted by 3 people Structural Biology Group TorVergata LOX-1 Receptor oteri
	Targeting the X-linked inhibitor of apoptosis protein through 4-substituted azabicyclo[5.3.0]alkane smac mimetics. Structure, activity, and recognition principles. [My Copy] Journal of molecular biology, Vol. 384, No. 3. (19 December 2008), pp. 673-689. by E. Mastrangelo, F. Cossu, M. Milani, et al.G. Sorrentino, D. Lecis, D. Delia, L. Manzoni, C. Drago, P. Seneci, C. Scolastico, V. Rizzo, M. Bolognesi posted by 3 people Structural Biology Group TorVergata oteri higueruelo
	Design, Synthesis, and Structure−Activity Relationship Studies of 3,4,6-Triphenylpyran-2-ones as Selective Cyclooxygenase-2 Inhibitors [My Copy] Journal of Medicinal Chemistry, Vol. 47, No. 16. (1 July 2004), pp. 3972-3990. by Praveen P. N. Rao, Md Uddin, Edward E. Knaus posted by 2 people Structural Biology Group TorVergata oteri
	Recognition in action: DNA mimicry. [My Copy] Journal of molecular recognition : JMR, Vol. 18, No. 6. (c 2005), pp. 427-430. by D. S. Goodsell posted by 2 people Structural Biology Group TorVergata oteri
	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 by 3 people znu Structural Biology Group TorVergata oteri
	LOX-1 abrogation reduces myocardial ischemia-reperfusion injury in mice. [My Copy] Journal of molecular and cellular cardiology, Vol. 44, No. 1. (January 2008), pp. 76-83. by C. Hu, J. Chen, A. Dandapat, et al.Y. Fujita, N. Inoue, Y. Kawase, K. Jishage, H. Suzuki, D. Li, P. L. Hermonat, T. Sawamura, J. L. Mehta posted by 2 people Structural Biology Group TorVergata oteri
	Domain-Based Decomposition Parallel Molecular Dynamics Algorithm on Computer Clusters [My Copy] Fuzzy Systems and Knowledge Discovery, 2007. FSKD 2007. Fourth International Conference on In Fuzzy Systems and Knowledge Discovery, 2007. FSKD 2007. Fourth International Conference on, Vol. 3 (2007), pp. 49-52. by Jiu-Ling Zhao, Jiu-Fen Zhao posted by 2 people Structural Biology Group TorVergata oteri
	[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 by 2 people Structural Biology Group TorVergata oteri
	Probing the Interaction between the Coiled Coil Leucine Zipper of cGMP-dependent Protein Kinase Ialpha and the C Terminus of the Myosin Binding Subunit of the Myosin Light Chain Phosphatase [My Copy] J. Biol. Chem., Vol. 283, No. 47. (21 November 2008), pp. 32860-32869. by Alok K. Sharma, Guo-Ping Zhou, Joseph Kupferman, et al.Howard K. Surks, Eva N. Christensen, James J. Chou, Michael E. Mendelsohn, Alan C. Rigby posted by 2 people Structural Biology Group TorVergata oteri
	Paranemic Cohesion of Topologically-Closed DNA Molecules [My Copy] Journal of the American Chemical Society, Vol. 124, No. 44. (1 November 2002), pp. 12940-12941. by Xiaoping Zhang, Hao Yan, Zhiyong Shen, Nadrian C. Seeman posted by 2 people Structural Biology Group TorVergata oteri
	Fragment molecular orbital method: application to polypeptides [My Copy] Chemical Physics Letters (March 2000), pp. 614-618. by T. Nakano, T. Kaminuma, T. Sato, Y. Akiyama, M. Uebayasi, K. Kitaura posted by 2 people Structural Biology Group TorVergata oteri
	Stability of DNA duplexes with Watson-Crick base pairs: a predicted model. [My Copy] Biochemistry, Vol. 43, No. 51. (28 December 2004), pp. 16467-16476. by M. Sundaralingam, P. K. Ponnuswamy posted by 2 people Structural Biology Group TorVergata oteri
	Derivatives of 5-Nitro-furan-2-carboxylic Acid Carbamoylmethyl Ester Inhibit RNase H Activity Associated with HIV-1 Reverse Transcriptase [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Hideyoshi Fuji, Emiko Urano, Yuko Futahashi, et al.Makiko Hamatake, Junko Tatsumi, Tyuji Hoshino, Yuko Morikawa, Naoki Yamamoto, Jun Komano posted by 2 people Structural Biology Group TorVergata oteri
	Discovery of (2S,4R)-1-(2-Aminoacetyl)-4-benzamidopyrrolidine-2-carboxylic Acid Hydrochloride (GAP-134)13, an Orally Active Small Molecule Gap-Junction Modifier for the Treatment of Atrial Fibrillation [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by John A. Butera, Bjarne D. Larsen, James K. Hennan, et al.Edward Kerns, Li Di, Asaf Alimardanov, Robert E. Swillo, Gwen A. Morgan, Kun Liu, Qiang Wang, Eric I. Rossman, Rayomand Unwalla, Leonard Mcdonald, Christine Huselton, Jørgen S. Petersen posted by 2 people Structural Biology Group TorVergata oteri
	Novel Indazole Non-Nucleoside Reverse Transcriptase Inhibitors Using Molecular Hybridization Based on Crystallographic Overlays† [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Lyn H. Jones, Gill Allan, Oscar Barba, et al.Catherine Burt, Romuald Corbau, Thomas Dupont, Thorsten Knöchel, Steve Irving, Donald S. Middleton, Charles E. Mowbray, Manos Perros, Heather Ringrose, Nigel A. Swain, Robert Webster, Mike Westby, Chris Phillips posted by 2 people Structural Biology Group TorVergata oteri
	NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106â126 [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 25. (9 December 2003), pp. 14790-14795. by Kazuo Kuwata, Tomoharu Matumoto, Hong Cheng, Kuniaki Nagayama, Thomas L. James, Heinrich Roder posted by 4 people pfluffernuugen Structural Biology Group TorVergata oteri scampos
	Deletion of LOX-1 Reduces Atherogenesis in LDLR Knockout Mice Fed High Cholesterol Diet [My Copy] Circ Res, Vol. 100, No. 11. (8 June 2007), pp. 1634-1642. by Jawahar L. Mehta, Nobuhito Sanada, Chang P. Hu, et al.Jiawei Chen, Abhijit Dandapat, Fumiaki Sugawara, Hiroo Satoh, Kazuhiko Inoue, Yosuke Kawase, Kou-Ichi Jishage, Hiroshi Suzuki, Motohiro Takeya, Laura Schnackenberg, Richard Beger, Paul L. Hermonat, Maria Thomas, Tatsuya Sawamura posted by 3 people Structural Biology Group TorVergata LOX-1 Receptor oteri
	The Levelwise Version Space Algorithm and its Application to Molecular Fragment Finding [My Copy] posted by 2 people Structural Biology Group TorVergata oteri
	Interfacing neurons with carbon nanotubes: electrical signal transfer and synaptic stimulation in cultured brain circuits. [My Copy] J Neurosci, Vol. 27, No. 26. (27 June 2007), pp. 6931-6936. by A. Mazzatenta, M. Giugliano, S. Campidelli, et al.L. Gambazzi, L. Businaro, H. Markram, M. Prato, L. Ballerini posted by 4 people tkf Structural Biology Group TorVergata oteri fbaroni
	The long coming of computational structural biology [My Copy] Journal of Structural Biology, Vol. 163, No. 3. (September 2008), pp. 254-257. by A. Lupas posted by 5 people stharward Structural Biology Group TorVergata oteri zwang psique personal
	ClusPro: Performance in CAPRI rounds 6-11 and the new server [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. 4. (2007), pp. 781-785. by Stephen R. Comeau, Dima Kozakov, Ryan Brenke, Yang Shen, Dmitri Beglov, Sandor Vajda posted by 2 people Structural Biology Group TorVergata oteri
	An Evolutionary Approach for Structure-based Design of Natural and Non-natural Peptidic Ligands [My Copy] Combinatorial Chemistry & High Throughput Screening (December 2001), pp. 661-673. by N. Budin, S. Ahmed, N. Majeux, A. Caflisch posted by 2 people Structural Biology Group TorVergata oteri
	Comparative analysis of coiled-coil prediction methods. [My Copy] Journal of structural biology, Vol. 155, No. 2. (August 2006), pp. 140-145. by Markus Gruber, Johannes Söding, Andrei N. Lupas posted by 7 people TLVincent kgutwin Structural Biology Group TorVergata oteri cjeans ca3295 marck
	UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation [My Copy] Nucl. Acids Res. (18 February 2009), gkp005. by Jinhao Zhu, Bryan Wei, Yuan Yuan, Yongli Mi posted by 2 people Structural Biology Group TorVergata oteri