medic0747's library 228 articles Export

	Estimates of the effect of natural selection on protein coding content [My Copy] Mol Biol Evol (8 October 2009), msp232. by Von B. Yap, Helen Lindsay, Simon Easteal, Gavin Huttley posted to selection protein evolution by medic0747 on 2009-10-09 08:37:18 as
	Comparative context analysis of codon pairs on an ORFeome scale [My Copy] Genome Biology, Vol. 6, No. 3. (2005), R28. by Gabriela Moura, Miguel Pinheiro, Raquel Silva, et al.Isabel Miranda, Vera Afreixo, Gaspar Dias, Adelaide Freitas, Jose Oliveira, Manuel Santos posted to codon by medic0747 on 2009-10-09 08:36:58 as
	Genomic DNA k-mer spectra: models and modalities [My Copy] Genome Biology, Vol. 10, No. 10. (2009), R108. by Benny Chor, David Horn, Yaron Levy, Nick Goldman, Tim Massingham posted to dna by medic0747 on 2009-10-08 12:31:44 as along with 3 people and 1 group djkt TRHvidsten gjuggler iSEEM
	PQS: a protein quaternary structure file server. [My Copy] Trends Biochem Sci, Vol. 23, No. 9. (September 1998), pp. 358-361. by K. Henrick, J. M. Thornton posted to protein quaternary server structure by medic0747 on 2009-06-17 19:43:54 as along with 3 people kgutwin bicko chad_davis
	MIPS: analysis and annotation of proteins from whole genomes. [My Copy] Nucleic Acids Res, Vol. 32 Database issue (1 January 2004) by H. W. Mewes, C. Amid, R. Arnold, et al.D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, A. Ruepp posted to database interaction protein-protein by medic0747 on 2009-06-17 19:41:01 as along with 3 people and 2 groups irenas lfriedl chad_davis dbk-lab kdl
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to force-field simulation by medic0747 on 2009-06-17 14:36:53 as along with 8 people and 1 group rodrigofaccioli mmuecke flbarroso jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	The GROMOS software for biomolecular simulation: GROMOS05 [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (2005), pp. 1719-1751. by Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, et al.Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren posted to force-field simulation by medic0747 on 2009-06-17 14:33:51 as
	ProTherm, version 2.0: thermodynamic database for proteins and mutants [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 283-285. by Michael M. Gromiha, Jianghong An, Hidetoshi Kono, et al.Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, Akinori Sarai posted to mutants protein stability thermodynamics by medic0747 on 2009-06-17 13:16:42 as
	Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis [My Copy] Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2002-2009. by Majid Masso, Iosif I. Vaisman posted to learning machine protein stability by medic0747 on 2009-06-17 12:05:56 as along with 4 people phoenixzxl zwang kluck afon
	Prediction of protein stability changes for single-site mutations using support vector machines. [My Copy] Proteins, Vol. 62, No. 4. (21 December 2005), pp. 1125-1132. by Jianlin Cheng, Arlo Randall, Pierre Baldi posted to learning machine protein stability svm by medic0747 on 2009-06-17 11:52:19 as along with 3 people bicko massivemayhem gisle
	I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by E. Capriotti, P. Fariselli, R. Casadio posted to learning machine protein stability svm by medic0747 on 2009-06-17 11:51:13 as along with 1 person gisle
	Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction [My Copy] Protein Science, Vol. 11, No. 11. (2002), pp. 2714-2726. by Hongyi Zhou, Yaoqi Zhou posted to protein stability by medic0747 on 2009-06-17 11:49:14 as
	Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. [My Copy] J Mol Biol, Vol. 307, No. 3. (30 March 2001), pp. 929-938. by J. Park, M. Lappe, S. A. Teichmann posted to interaction protein-protein by medic0747 on 2009-06-15 15:16:35 as along with 5 people and 2 groups chad_davis ronkeliz ana tjimenez cjeans structural_bioinformatics Bioinformatics
	Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect [My Copy] Protein Science, Vol. 6, No. 1. (1997), pp. 53-64. by Chung-Jung Tsai, Shuo L. Lin, Haim J. Wolfson, Ruth Nussinov posted to analysis interface protein-protein by medic0747 on 2009-06-15 14:31:12 as
	Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis. [My Copy] Proteins, Vol. 77, No. 1. (October 2009), pp. 84-96. by Julia R. Forman, Catherine L. Worth, G. Richard Bickerton, Tim G. Eisen, Tom L. Blundell posted to correlation disease mutation protein by medic0747 on 2009-06-09 16:04:11 as along with 2 people and 1 group AliC bicko Orengo Group Journal Picks
	Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. [My Copy] Protein Sci, Vol. 13, No. 7. (July 2004), pp. 1865-1874. by V. A. Ilyin, A. Abyzov, C. M. Leslin posted to alignment protein structure by medic0747 on 2009-06-09 13:33:17 as along with 3 people and 2 groups reyez ana analogAI structural_bioinformatics Bioinformatics
	TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method [My Copy] Nucleic Acids Research, Vol. 35, No. Supplement 1. (January 2007), pp. D317-D321. by Leslin, M. Chesley, Abyzov, Alexej, Ilyin, A. Valentin posted to alignment database protein structural by medic0747 on 2009-06-09 12:47:31 as
	The ENZYME database in 2000 [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 304-305. by Amos Bairoch posted to database enzyme protein by medic0747 on 2009-06-09 12:44:38 as along with 4 people incovoma shung carlk grottenolm
	A New Algorithm For The Alignment Of Multiple Protein Structures Using Monte Carlo Optimization [My Copy] Pac. Symp. Biocomput, Vol. 6 (2001), pp. 275-286. by C. Guda, E. D. Scheeff, P. E. Bourne, I. N. Shindyalov posted to algorithm alignment multiple protein structure by medic0747 on 2009-06-09 12:31:40 as
	DMAPS: a database of multiple alignments for protein structures. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006) by C. Guda, L. R. Pal, I. N. Shindyalov posted to alignment multiple protein structure by medic0747 on 2009-06-09 12:29:18 as
	Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. [My Copy] Protein Eng, Vol. 11, No. 9. (September 1998), pp. 739-747. by I. N. Shindyalov, P. E. Bourne posted to alignment protein structure by medic0747 on 2009-06-09 12:25:50 as along with 11 people and 2 groups sebk reyez pjcite nigham jwm analogAI dgront rabio siebertm Inchoate sim82 Radiation_Damage Stressosome
	DBAli: a database of protein structure alignments. [My Copy] Bioinformatics, Vol. 17, No. 8. (August 2001), pp. 746-747. by M. A. Martí-Renom, V. A. Ilyin, A. Sali posted to alignment database protein structure by medic0747 on 2009-06-09 11:55:13 as along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
	T-Coffee: A novel method for fast and accurate multiple sequence alignment. [My Copy] Journal of molecular biology, Vol. 302, No. 1. (8 September 2000), pp. 205-217. by C. Notredame, D. G. Higgins, J. Heringa posted to alignment multiple protein sequence by medic0747 on 2009-06-09 11:51:23 as along with 17 people and 1 group bratwurst viktor21614 tomjad robert laurabailey BioNica sebk miguel dayjm indigoviolet ffranca treangen Haggan siebertm adijr marti newton1234 EisenLab
	Protein structure comparison using SAP. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 143 (2000), pp. 19-32. by W. R. Taylor posted to comparison protein structure by medic0747 on 2009-06-09 11:48:23 as
	S4: structure-based sequence alignments of SCOP superfamilies [My Copy] Nucleic Acids Research, Vol. 33, No. Supplement 1. (1 January 2005), D219. by James Casbon, Mansoor A. S. Saqi posted to alignment database protein structure by medic0747 on 2009-06-09 11:39:08 as
	A systematic comparison of protein structure classifications: SCOP, CATH and FSSP [My Copy] Structure, Vol. 7, No. 9. (15 September 1999), pp. 1099-1112. by Caroline Hadley, David T. Jones posted to classification protein structure by medic0747 on 2009-06-09 11:33:11 as along with 1 person yuslinaz
	PROCHECK: a program to check the stereochemical quality of protein structures [My Copy] Journal of Applied Crystallography, Vol. 26, No. 2. (Apr 1993), pp. 283-291. by R. A. Laskowski, M. W. Macarthur, D. S. Moss, J. M. Thornton posted to evaluation protein structure by medic0747 on 2009-06-08 16:03:59 as
	Recognition of errors in three-dimensional structures of proteins. [My Copy] Proteins, Vol. 17, No. 4. (December 1993), pp. 355-362. by M. J. Sippl posted to evaluation protein structure by medic0747 on 2009-06-08 16:00:54 as along with 2 people j3xucite hmk
	Assessing protein structures with a non-local atomic interaction energy. [My Copy] J Mol Biol, Vol. 277, No. 5. (17 April 1998), pp. 1141-1152. by F. Melo, E. Feytmans posted to evaluation model protein structure by medic0747 on 2009-06-08 15:57:57 as along with 1 person dgront
	An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase [My Copy] Journal of Computational Chemistry, Vol. 22, No. 11. (2001), pp. 1205-1218. by Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren posted to field force by medic0747 on 2009-06-08 15:46:31 as along with 3 people peyamin tovrstra ashaytan
	SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling [My Copy] Electrophoresis, Vol. 18, No. 15. (1997), pp. 2714-2723. by Nicolas Guex, Manuel C. Peitsch posted to comparative homology modeling protein structure viewer by medic0747 on 2009-06-08 15:40:26 as along with 3 people chiufanlee mikelape ubcg08l
	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 homology modeling protein by medic0747 on 2009-06-08 14:29:01 as along with 3 people tjimenez noraziz chad_davis
	A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. [My Copy] J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 241-254. by K. Robison, A. M. McGuire, G. M. Church posted to database dna interaction protein by medic0747 on 2009-06-08 13:52:21 as along with 2 people kaarsinogen nklee
	Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. [My Copy] Chemistry & biology, Vol. 3, No. 12. (December 1996), pp. 973-980. by J. E. Ladbury posted to interaction ligand protein water by medic0747 on 2009-06-08 13:27:20 as
	E-MSD: an integrated data resource for bioinformatics. [My Copy] Nucleic acids research, Vol. 33, No. Database issue. (1 January 2005), D262. by S. Velankar, P. McNeil, V. Mittard-Runte, et al.A. Suarez, D. Barrell, R. Apweiler, K. Henrick posted to database structure by medic0747 on 2009-06-08 13:11:55 as along with 1 person bicko
	A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742. by N. D. Gold, R. M. Jackson posted to database interaction ligand protein by medic0747 on 2009-06-08 13:07:56 as along with 4 people and 1 group caporaso blackbart massivemayhem reyez biomedical-nlp
	LIGAND: database of chemical compounds and reactions in biological pathways. [My Copy] Nucleic Acids Res, Vol. 30, No. 1. (1 January 2002), pp. 402-404. by S. Goto, Y. Okuno, M. Hattori, T. Nishioka, M. Kanehisa posted to database interaction ligand protein by medic0747 on 2009-06-08 13:00:46 as along with 7 people alexg blackbart koerner massivemayhem dagmar shung sim82
	STITCH: interaction networks of chemicals and proteins [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_1. (11 January 2008), pp. D684-688. by Michael Kuhn, Christian von Mering, Monica Campillos, Lars J. Jensen, Peer Bork posted to database interaction ligand protein by medic0747 on 2009-06-08 12:58:51 as along with 9 people and 1 group mitko Cortel guhjy balicea massivemayhem bootsy sobolevnrm larsjuhljensen higueruelo baker-group
	Protein ligand interaction database (PLID). [My Copy] Computational biology and chemistry, Vol. 32, No. 5. (October 2008), pp. 387-390. by A. Srinivas Reddy, Durga S. Amarnath, Raju S. Bapi, G. Madhavi Sastry, G. Narahari Sastry posted to database interaction ligand protein by medic0747 on 2009-06-08 11:37:35 as along with 3 people oceanwind guhjy zwang
	Binding MOAD, a high-quality protein-ligand database. [My Copy] Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008) by M. L. Benson, R. D. Smith, N. A. Khazanov, et al.B. Dimcheff, J. Beaver, P. Dresslar, J. Nerothin, H. A. Carlson posted to database ligand protein by medic0747 on 2009-06-08 11:36:25 as along with 6 people pauldobson reyez nickolay massivemayhem higueruelo guhjy
	PROCAIN server for remote protein sequence similarity search [My Copy] Bioinformatics, Vol. 25, No. 16. (15 August 2009), pp. 2076-2077. by Yong Wang, Ruslan I. Sadreyev, Nick V. Grishin posted to homology protein sequence server similarity by medic0747 on 2009-06-06 11:13:45 as along with 4 people and 1 group kshameer reyez carlosjavierna phoenixzxl Journal picks
	On the Origins of Enzyme Inhibitor Selectivity and Promiscuity: A Case Study of Protein Kinase Binding to Staurosporine [My Copy] Chemical Biology & Drug Design, Vol. 74, No. 1. (2009), in press. by Duangrudee Tanramluk, Adrian Schreyer, William R. Pitt, Tom L. Blundell posted to no-tag by medic0747 on 2009-06-01 16:08:38 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 ligand recognition search shape by medic0747 on 2009-06-01 11:46:21 as along with 5 people operon massivemayhem ssgong kintoki tjimenez
	Ulla: a program for calculating environment-specific amino acid substitution tables [My Copy] Bioinformatics (5 May 2009), btp300. by Semin Lee, Tom L. Blundell posted to acid amino mutation protein substitution by medic0747 on 2009-06-01 11:42:12 as along with 1 person operon
	BIPA: a database for protein-nucleic acid interaction in 3D structures. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. 1559-1560. by S. Lee, T. L. Blundell posted to acid database interaction nucleic protein structure by medic0747 on 2009-06-01 11:41:48 as along with 3 people higueruelo scjparker phoenixzxl
	Fold assessment for comparative protein structure modeling. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 11. (November 2007), pp. 2412-2426. by F. Melo, A. Sali posted to modeling protein structure by medic0747 on 2009-06-01 09:59:50 as
	Small Molecule Protein–Protein Interaction Inhibitors as CNS Therapeutic Agents: Current Progress and Future Hurdles [My Copy] Neuropsychopharmacology, Vol. aop, No. current. by Levi L. Blazer, Richard R. Neubig posted to no-tag by medic0747 on 2009-03-17 16:28:23 as along with 3 people semin calvin higueruelo
	The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome [My Copy] Genome Research (1 January 2009) by Subhajyoti De, Sarah A. Teichmann, Madan M. Babu posted to evolution genome by medic0747 on 2009-02-20 09:34:02 as along with 12 people and 1 group mox natstreet clearbluespring maximilianh djkt alweber jbhiatt xianjun cisevol inesdesantiago provero JustinCrocker cis-regulatory-evolution
	Models of coding sequence evolution. [My Copy] Briefings in bioinformatics, Vol. 10, No. 1. (1 January 2009), pp. 97-109. by Wayne Delport, Konrad Scheffler, Cathal Seoighe posted to evolution molecular sequence by medic0747 on 2009-01-31 12:49:56 as along with 10 people operon BioNica katholt chica dakelley nuin michaelbarton treangen druvus nklee
	Conserved domains in DNA repair proteins and evolution of repair systems [My Copy] Nucl. Acids Res., Vol. 27, No. 5. (1 March 1999), pp. 1223-1242. by L. Aravind, D. R. Walker, E. V. Koonin posted to evolution interaction protein-dna by medic0747 on 2007-09-26 14:58:35 as along with 1 person robfsouza

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protein	120
interaction	87
tlb	67
protein-dna	57
modeling	24
structure	23
database	16
evolution	12
acid	10
alignment	9
classification	9
nucleic	9
protein-rna	9
esst	8
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hydrogen	6
stability	6
loop	5
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exon	4
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evaluation	3
learning	3
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water	2
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atom	1
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detection	1
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docking	1
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enzyme	1
eta	1
field	1
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force	1
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model	1
molecular	1
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qtl	1
quaternary	1
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search	1
selection	1
shape	1
similarity	1
statistical	1
structural	1
substitution	1
surface	1
thermodynamics	1
vdw	1
viewer	1

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