tjimenez's library 255 articles Export

	MODBASE, a database of annotated comparative protein structure models, and associated resources. [My Copy] Nucleic acids research, Vol. 32, No. Database issue. (1 January 2004) by Ursula Pieper, Narayanan Eswar, Hannes Braberg, et al.M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali posted to comparative_protein_structure by tjimenez on 2009-10-27 18:00:17 as along with 4 people and 2 groups pjcite marcius dgront blackbart BioinfoCIPF SGU-CIPF
	MODBASE, a database of annotated comparative protein structure models and associated resources. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (23 January 2009) by Ursula Pieper, Narayanan Eswar, Ben M. Webb, et al.David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Marti-Renom, Fred P. Davis, Andrej Sali posted to comparative_protein_structure by tjimenez on 2009-10-27 17:59:43 as along with 3 people noraziz medic0747 chad_davis
	Comparative protein structure modeling of genes and genomes. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 29 (2000), pp. 291-325. by M. A. Martí-Renom, A. C. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali posted to molecular_comparison by tjimenez on 2009-10-27 17:56:38 as along with 15 people and 2 groups jperkins fautore aalibes nigham chad_davis ttjoseph marcius ffranca duartemolha dgront ruvido insectopalo min013 IrinaMoreira granujilla BioinfoCIPF SGU-CIPF
	MSDmotif: exploring protein sites and motifs [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 312. by Adel Golovin, Kim Henrick posted to structure_to_function by tjimenez on 2008-11-11 20:54:32 as along with 6 people pansapiens HawkinsJohnC reyez massivemayhem chad_davis Evangelia
	Recognizing the fold of a protein structure. [My Copy] Bioinformatics (Oxford, England), Vol. 19, No. 14. (22 September 2003), pp. 1748-1759. by Andrew Harrison, Frances Pearl, Ian Sillitoe, et al.Tim Slidel, Richard Mott, Janet Thornton, Christine Orengo posted to structure_to_function by tjimenez on 2008-11-11 19:05:30 as along with 2 people and 1 group sillitoe AbnerCYH Orengo Group Journal Picks
	A new bioinformatic approach to detect common 3D sites in protein structures. [My Copy] Proteins, Vol. 52, No. 2. (1 August 2003), pp. 137-145. by M. Jambon, A. Imberty, G. Deléage, C. Geourjon posted to structure_to_function by tjimenez on 2008-11-11 18:58:15 as along with 1 person tomjad
	Functional sites in protein families uncovered via an objective and automated graph theoretic approach. [My Copy] Journal of molecular biology, Vol. 326, No. 3. (21 February 2003), pp. 955-978. by P. P. Wangikar, A. V. Tendulkar, S. Ramya, D. N. Mali, S. Sarawagi posted to structure_to_function by tjimenez on 2008-11-11 18:55:45 as
	The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data [My Copy] Nucl. Acids Res., Vol. 32, No. suppl_1. (1 January 2004), pp. D129-133. by Craig T. Porter, Gail J. Bartlett, Janet M. Thornton posted to structure_to_function by tjimenez on 2008-11-11 18:52:35 as along with 12 people and 2 groups barmak7282 ucbcjbm pablocarb baaden chrn jwm gbart tny sriram_s massivemayhem siebertm grottenolm Radiation_Damage Stressosome
	Prediction of functional sites in proteins using conserved functional group analysis. [My Copy] J Mol Biol, Vol. 337, No. 4. (2 April 2004), pp. 1053-1068. by C. A. Innis, A. P. Anand, R. Sowdhamini posted to structure_to_function by tjimenez on 2008-11-11 18:50:32 as along with 2 people chrn mingzhi
	Protein structure comparison by alignment of distance matrices. [My Copy] Journal of molecular biology, Vol. 233, No. 1. (5 September 1993), pp. 123-138. by L. Holm, C. Sander posted to structure_to_function by tjimenez on 2008-11-11 18:48:51 as along with 7 people and 2 groups jwm BragilMassoud ana nigham dgront siebertm sim82 structural_bioinformatics Bioinformatics
	Protein homology detection by HMM-HMM comparison. [My Copy] Bioinformatics (Oxford, England), Vol. 21, No. 7. (1 April 2005), pp. 951-960. by Johannes Söding posted to sequence_similarity by tjimenez on 2008-11-11 18:47:42 as along with 3 people grottenolm maria_hauser j3xucite
	Rapid and sensitive protein similarity searches. [My Copy] Science (New York, N.Y.), Vol. 227, No. 4693. (22 March 1985), pp. 1435-1441. by D. J. Lipman, W. R. Pearson posted to sequence_similarity by tjimenez on 2008-11-11 18:34:31 as along with 4 people c_hughes dgront CitoJam lusk
	Basic local alignment search tool [My Copy] Journal of Molecular Biology, Vol. 215 (1990), pp. 403-410. by S. F. Altschul, W. Gish, W. Miller, E. W. Myers, D. J. Lipman posted to sequence_similarity by tjimenez on 2008-11-07 19:28:17 as
	Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. [My Copy] Nucleic acids research, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402. by S. F. Altschul, T. L. Madden, A. A. Schäffer, et al.J. Zhang, Z. Zhang, W. Miller, D. J. Lipman posted to sequence_similarity by tjimenez on 2008-11-07 19:21:41 as along with 68 people and 5 groups rshe niallhaslam ucbcjbm timhubbard parnell tfuji maria_hauser jbhiatt yylin mgomes BioNica idoerg pjcite swp09 kgutwin mcbla cpwardell johanviklund daforerog nlapalu sebk shung pwais dakelley knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver david_parsons indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 mijam grottenolm bandrewfox edvin newton1234 mariakmejia granujilla marti CharlesM References for 3DSim paper EisenLab biomedical-nlp Microbial-Ecology Plantandetc
	Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111. by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton posted to function knowledge-based_potentials molecular_comparison structure_to_function by tjimenez on 2008-10-14 18:06:05 as along with 7 people iaolier krapnik ramensky apaydin neils reyez nickolay
	Comparison of correlation vector methods for ligand-based similarity searching. [My Copy] Journal of computer-aided molecular design, Vol. 17, No. 10. (October 2003), pp. 687-698. by U. Fechner, L. Franke, S. Renner, P. Schneider, G. Schneider posted to autocorrelation molecular_comparison by tjimenez on 2008-08-19 19:07:09 as
	Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as alternative attractive tool to generate ligand-based 3D-QSARs. [My Copy] Current drug discovery technologies, Vol. 2, No. 1. (March 2005), pp. 13-21. by S. Moro, M. Bacilieri, C. Ferrari, G. Spalluto posted to autocorrelation molecular_comparison by tjimenez on 2008-08-19 18:53:41 as
	Locating biologically active compounds in medium-sized heterogeneous datasets by topological autocorrelation vectors: dopamine and benzodiazepine agonists. [My Copy] Journal of chemical information and computer sciences, Vol. 36, No. 6. (c 1996), pp. 1205-1213. by H. Bauknecht, A. Zell, H. Bayer, et al.P. Levi, M. Wagener, J. Sadowski, J. Gasteiger posted to autocorrelation molecular_comparison by tjimenez on 2008-08-19 18:47:46 as
	Molecular structures: perception, autocorrelation descriptor and sar studies. Autocorrelation descriptor [My Copy] European journal of medicinal chemistry, Vol. 19, No. 1. (1984), pp. 66-70. by P. Broto, G. Moreau, C. Vandycke posted to autocorrelation molecular_comparison by tjimenez on 2008-08-19 16:56:25 as
	MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. [My Copy] Protein science : a publication of the Protein Society, Vol. 11, No. 11. (1 November 2002), pp. 2606-2621. by Angel R. Ortiz, Charlie E. Strauss, Osvaldo Olmea posted to alignment structural by tjimenez on 2008-08-10 10:09:38 as along with 8 people and 2 groups tomjad awarlau ana iakes dimka jwm analogAI sebk structural_bioinformatics Bioinformatics
	A new progressive-iterative algorithm for multiple structure alignment. [My Copy] Bioinformatics (7 June 2005) by Dmitry Lupyan, Alejandra Leo-Macias, Angel R R. Ortiz posted to alignment structural by tjimenez on 2008-08-10 10:09:22 as along with 5 people and 4 groups tomjad sebk ana dimka marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Automatic methods for predicting functionally important residues. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1289-1302. by A. del Sol Mesa, F. Pazos, A. Valencia posted to sequence_similarity by tjimenez on 2008-08-09 19:05:48 as along with 2 people kaarsinogen nickolay
	Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families [My Copy] Protein Sci, Vol. 13, No. 2. (1 February 2004), pp. 443-456. by Olga V. Kalinina, Andrey A. Mironov, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova posted to sequence_similarity by tjimenez on 2008-08-09 19:02:14 as along with 1 person sriram_s
	Gene fusions and gene duplications: relevance to genomic annotation and functional analysis. [My Copy] BMC Genomics, Vol. 6, No. 1. (9 March 2005) by M. H. Serres, M. Riley posted to sequence_similarity by tjimenez on 2008-08-09 19:01:20 as along with 1 person tmmurali
	Using orthologous and paralogous proteins to identify specificity determining residues. [My Copy] Genome biology, Vol. 3, No. 3. (2002) by L. A. Mirny, M. S. Gelfand posted to sequence_similarity by tjimenez on 2008-08-09 19:00:35 as
	Parallel screening: a novel concept in pharmacophore modeling and virtual screening. [My Copy] J Chem Inf Model, Vol. 46, No. 5. (t 2006), pp. 2146-2157. by T. M. Steindl, D. Schuster, C. Laggner, T. Langer posted to selectivity by tjimenez on 2008-08-09 17:56:30 as along with 2 people jbhonsle apostola
	Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. [My Copy] Journal of chemical information and modeling, Vol. 46, No. 3. (n 2006), pp. 1124-1133. by Nidhi, M. Glick, J. W. Davies, J. L. Jenkins posted to selectivity by tjimenez on 2008-08-09 17:54:51 as
	Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors. [My Copy] J Med Chem, Vol. 49, No. 23. (16 November 2006), pp. 6802-6810. by J. H. Nettles, J. L. Jenkins, A. Bender, Z. Deng, J. W. Davies, M. Glick posted to selectivity by tjimenez on 2008-08-09 17:53:35 as along with 1 person kuhn
	Ligand-based approach to in silico pharmacology: nuclear receptor profiling. [My Copy] Journal of chemical information and modeling, Vol. 46, No. 6. (c 2006), pp. 2725-2736. by J. Mestres, L. Martín-Couce, E. Gregori-Puigjané, M. Cases, S. Boyer posted to selectivity by tjimenez on 2008-08-09 17:52:25 as
	Substructure-based support vector machine classifiers for prediction of adverse effects in diverse classes of drugs. [My Copy] Journal of chemical information and modeling, Vol. 46, No. 6. (c 2006), pp. 2478-2486. by S. Bhavani, A. Nagargadde, A. Thawani, V. Sridhar, N. Chandra posted to selectivity by tjimenez on 2008-08-09 17:50:11 as
	"Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept? [My Copy] Journal of chemical information and modeling, Vol. 46, No. 6. (c 2006), pp. 2445-2456. by A. Bender, J. L. Jenkins, M. Glick, Z. Deng, J. H. Nettles, J. W. Davies posted to selectivity by tjimenez on 2008-08-09 17:48:39 as
	Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family. [My Copy] Current topics in medicinal chemistry, Vol. 5, No. 8. (2005), pp. 763-772. by M. Cases, R. García-Serna, K. Hettne, et al.M. Weeber, J. van der Lei, S. Boyer, J. Mestres posted to selectivity by tjimenez on 2008-08-09 17:47:10 as
	Chemogenomic approaches to rational drug design [My Copy] Br J Pharmacol, Vol. 152, No. 1. (29 May 2007), pp. 38-52. by D. Rognan posted to selectivity by tjimenez on 2008-08-09 17:06:59 as along with 4 people and 3 groups xdeupi jmrivort jerome_ucsf_slb guhjy LabCompMed G-quadruplex Supramolecular
	Large-scale prediction of drug-target relationships. [My Copy] FEBS letters, Vol. 582, No. 8. (9 April 2008), pp. 1283-1290. by M. Kuhn, M. Campillos, P. González, L. J. Jensen, P. Bork posted to molecular_comparison selectivity by tjimenez on 2008-08-08 11:35:45 as along with 3 people daforerog mitko larsjuhljensen
	Computational analysis of ligand relationships within target families [My Copy] Current Opinion in Chemical Biology, Vol. In Press, Corrected Proof by Jurgen Bajorath posted to kinase selectivity by tjimenez on 2008-08-08 11:24:57 as along with 1 person jerome_ucsf_slb
	Chemical Fragments as Foundations for Understanding Target Space and Activity Prediction [My Copy] Journal of Medicinal Chemistry, Vol. 51, No. 9. (1 May 2008), pp. 2689-2700. by Jeffrey J. Sutherland, Richard E. Higgs, Ian Watson, Michal Vieth posted to kinase selectivity by tjimenez on 2008-08-04 07:35:39 as
	Generalized solvent boundary potential for computer simulations [My Copy] Journal of chemical physics, Vol. 114, No. 7. (15 February 2001), pp. 2924-2937. by W. Im, S. Berneche, B. Roux posted to harmonics shape by tjimenez on 2008-05-09 10:45:06 as
	Ultrafast shape recognition to search compound databases for similar molecular shapes. [My Copy] J Comput Chem (6 March 2007) by Pedro J J. Ballester, W Graham G. Richards posted to shape by tjimenez on 2008-05-09 09:29:49 as along with 5 people medic0747 operon massivemayhem ssgong kintoki
	SHEF: a vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. [My Copy] Journal of molecular modeling, Vol. 14, No. 5. (May 2008), pp. 393-401. by W. Cai, J. Xu, X. Shao, V. Leroux, A. Beautrait, B. Maigret posted to harmonics by tjimenez on 2008-05-07 18:37:45 as
	Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening. [My Copy] Journal of molecular graphics & modelling, Vol. 20, No. 4. (January 2002), pp. 313-328. by W. Cai, X. Shao, B. Maigret posted to harmonics by tjimenez on 2008-05-07 18:36:05 as
	An evaluation of spherical designs for molecular-like surfaces. [My Copy] Journal of molecular graphics & modelling, Vol. 24, No. 5. (March 2006), pp. 356-361. by R. J. Morris posted to harmonics by tjimenez on 2008-05-07 18:34:57 as
	An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties. [My Copy] Journal of chemical information and modeling, Vol. 45, No. 4. (g 2005), pp. 1010-1016. by J. H. Lin, T. Clark posted to harmonics by tjimenez on 2008-05-07 18:32:09 as
	Molecular shape and electrostatics in the encoding of relevant chemical information. [My Copy] Journal of computer-aided molecular design, Vol. 19, No. 9-10. (t 2005), pp. 661-686. by A. Nicholls, J. A. Grant posted to comparison shape by tjimenez on 2008-05-07 18:30:21 as along with 1 person flbarroso
	A Fast Method of Molecular Shape Comparison: A Simple Application of a Gaussian Description of Molecular Shape. [My Copy] Journal of computational chemistry, Vol. 17, No. 14. (1996), pp. 1653-1666. by J. A. Grant, M. A. Gallardo, B. T. Pickup posted to comparison shape by tjimenez on 2008-05-07 18:27:31 as
	Toward High Throughput 3D Virtual Screening Using Spherical Harmonic Surface Representations [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 5. (1 September 2007), pp. 1787-1796. by Lazaros Mavridis, Brian D. Hudson, David W. Ritchie posted to harmonics by tjimenez on 2008-05-07 17:50:25 as along with 1 person ubcg08l
	Shape Variation in Protein Binding Pockets and their Ligands. [My Copy] J Mol Biol, Vol. 368, No. 1. (20 April 2007), pp. 283-301. by A. Kahraman, R. J. Morris, R. A. Laskowski, J. M. Thornton posted to harmonics by tjimenez on 2008-05-07 17:48:41 as along with 4 people babakap grottenolm martainn jwm
	An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. [My Copy] Journal of molecular graphics & modelling, Vol. 26, No. 7. (April 2008), pp. 1035-1045. by L. Mak, S. Grandison, R. J. Morris posted to harmonics by tjimenez on 2008-05-07 11:38:53 as
	Rotation invariant spherical harmonic representation of 3D shape descriptors [My Copy] (2003) by M. Kazhdan, T. Funkhouser, S. Rusinkiewicz posted to harmonics by tjimenez on 2008-05-07 11:14:38 as
	Moment invariants as shape recognition technique for comparing protein binding sites [My Copy] Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3139-3146. by Ingolf Sommer, Oliver Muller, Francisco S. Domingues, Oliver Sander, Joachim Weickert, Thomas Lengauer posted to shape by tjimenez on 2008-05-05 18:58:43 as along with 1 person carlescorbi
	Efficient shape descriptors for feature extraction in 3D protein structures. [My Copy] In silico biology, Vol. 7, No. 2. (2007), pp. 169-174. by A. Ranganath, K. C. Shet, N. Vidyavathi posted to shape by tjimenez on 2008-05-05 18:55:22 as

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structure_to_function	45
kinase	41
binding_pocket_recognition	34
scop_cath	19
harmonics	16
selectivity	13
molecular_comparison	12
superimposition	12
sequence_similarity	11
clique	10
shape	8
geometric_hashing	6
autocorrelation	4
comparison	4
knowledge-based_potentials	4
pose_clustering	4
tim_barrel	4
docking	3
fourier	3
homology	3
models	3
tops	3
alfa-shape	2
alignment	2
binding	2
comparative_protein_structure	2
function	2
rotational_matching	2
sites	2
structural	2
superstar	2
classification	1
druggability	1
family	1
gaussian	1
graph	1
jelly_roll	1
neural_networks	1
protein_interactions	1
sequence	1
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tjimenez's library 255 articles Export

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