marcius's computational_biology [53 articles] Export

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	Sampling Realistic Protein Conformations Using Local Structural Bias [My Copy] PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e131. by Thomas Hamelryck, John T. Kent, Anders Krogh posted to biophysics clustering computational_biology dynamics structure by marcius on 2006-09-29 08:57:03 as along with 1 person and 2 groups mijam BioinfoCIPF SGU-CIPF
	Physical Origins of Protein Superfamilies. [My Copy] J Mol Biol (6 February 2006) by Konstantin B B. Zeldovich, Igor N N. Berezovsky, Eugene I I. Shakhnovich posted to biophysics computational_biology evolution protein structure by marcius on 2006-04-27 20:29:04 as along with 3 people and 3 groups Einat laurabailey happy_manatee structural_bioinformatics BioinfoCIPF SGU-CIPF
	Predicting free energy landscapes for complexes of double-stranded chain molecules [My Copy] The Journal of Chemical Physics, Vol. 114, No. 9. (2001), pp. 4253-4266. by Wenbing Zhang, Shi J. Chen posted to biophysics computational_biology dna folding rna by marcius on 2006-04-21 22:11:14 as along with 1 person and 3 groups condon beta BioinfoCIPF SGU-CIPF
	Theory for the conformational changes of double-stranded chain molecules [My Copy] The Journal of Chemical Physics, Vol. 109, No. 11. (1998), pp. 4602-4616. by Shi J. Chen, Ken A. Dill posted to biophysics computational_biology dna folding rna by marcius on 2006-04-21 22:11:01 as along with 1 person and 3 groups condon beta BioinfoCIPF SGU-CIPF
	Statistical thermodynamics of double-stranded polymer molecules [My Copy] The Journal of Chemical Physics, Vol. 103, No. 13. (1995), pp. 5802-5813. by Shi J. Chen, Ken A. Dill posted to biophysics computational_biology dna folding rna by marcius on 2006-04-21 22:10:14 as along with 1 person and 3 groups condon beta BioinfoCIPF SGU-CIPF
	2020 Computing: Can computers help to explain biology? [My Copy] Nature, Vol. 440, No. 7083. (22 March 2006), pp. 416-417. by Roger Brent, Jehoshua Bruck posted to computational_biology views by marcius on 2006-03-28 06:30:11 as along with 7 people and 2 groups karthikraman vkwn cmmorel eweaver ddahlem dullhunk bigbossman BioinfoCIPF SGU-CIPF
	Evidence that miRNAs are different from other RNAs. [My Copy] Cell Mol Life Sci, Vol. 63, No. 2. (January 2006), pp. 246-254. by B. H. Zhang, X. P. Pan, S. B. Cox, G. P. Cobb, T. A. Anderson posted to biophysics computational_biology microrna by marcius on 2006-03-17 18:48:36 as along with 4 people and 6 groups eckart_bindewald andersbj dchughes cdawson microRNA G4ID BioinfoCIPF SGU-CIPF GIG Genetics-of-Gambling
	Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency [My Copy] RNA, Vol. 11, No. 5. (1 May 2005), pp. 578-591. by Peter Clote, Fabrizio Ferre, Evangelos Kranakis, Danny Krizanc posted to computational_biology folding rna by marcius on 2006-03-17 07:35:58 as along with 3 people and 2 groups NicholasErho arcticrasta elfar BioinfoCIPF SGU-CIPF
	Computer-aided NMR assay for detecting natively folded structural domains. [My Copy] Protein Sci (7 March 2006) by Takayuki Hondoh, Atsushi Kato, Shigeyuki Yokoyama, Yutaka Kuroda posted to computational_biology nmr protein_domains by marcius on 2006-03-15 23:01:54 as along with 2 groups BioinfoCIPF SGU-CIPF
	Towards genome-scale structure prediction for transmembrane proteins. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 465-475. by N. Hurwitz, M. Pellegrini-Calace, D. T. Jones posted to computational_biology membrane_protein structure_prediction by marcius on 2006-03-15 22:59:20 as along with 1 person and 2 groups thaliana BioinfoCIPF SGU-CIPF
	Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space. [My Copy] Proteins, Vol. 50, No. 1. (1 January 2003), pp. 35-43. by S. Miyazawa, R. L. Jernigan posted to computational_biology model_assessment statistical_potentials by marcius on 2006-03-07 18:44:30 as along with 1 person and 4 groups ana structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. [My Copy] Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 6057-6069. by U. Laserson, H. H. Gan, T. Schlick posted to computational_biology function genome ncrna rna by marcius on 2006-03-06 22:49:02 as along with 2 groups BioinfoCIPF SGU-CIPF
	Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes [My Copy] Nature Biotechnology, Vol. 23, No. 11. (23 October 2005), pp. 1424-1433. by Robert Penchovsky, Ronald R. Breaker posted to computational_biology ncrna by marcius on 2006-03-06 22:33:55 as along with 4 people and 2 groups reyez rklancer dbikard austin BioinfoCIPF SGU-CIPF
	RNAshapes: an integrated RNA analysis package based on abstract shapes [My Copy] Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 500-503. by Peter Steffen, Bjorn Voss, Marc Rehmsmeier, Jens Reeder, Robert Giegerich posted to bioinformatics computational_biology rna secondary_structure by marcius on 2006-02-16 18:13:15 as along with 2 people and 2 groups penka Hosna BioinfoCIPF SGU-CIPF
	Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets [My Copy] Cell, Vol. 120, No. 1. (14 January 2005), pp. 15-20. by Benjamin P. Lewis, Christopher B. Burge, David P. Bartel posted to bioinformatics computational_biology microrna ncrna by marcius on 2006-02-13 20:24:00 as along with 14 people and 3 groups danaiancu sterovetta ronglais pengchy jfr maryee eckart_bindewald tardigrade mortenlindow andersbj mtagaya heliopais Alexander_Kanitz elfar microRNA BioinfoCIPF SGU-CIPF
	Modeling the three-dimensional structure of RNA. [My Copy] FASEB J, Vol. 7, No. 1. (January 1993), pp. 97-105. by D. Gautheret, R. Cedergren posted to computational_biology rna structure_prediction by marcius on 2006-02-11 01:12:07 as along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
	Computational genomics of noncoding RNA genes. [My Copy] Cell, Vol. 109, No. 2. (19 April 2002), pp. 137-140. by S. R. Eddy posted to computational_biology microrna review by marcius on 2006-02-10 21:09:57 as along with 4 people and 2 groups NicholasErho antonkratz myrtilus arcticrasta BioinfoCIPF SGU-CIPF
	Computational identification of noncoding RNAs in E. coli by comparative genomics. [My Copy] Curr Biol, Vol. 11, No. 17. (4 September 2001), pp. 1369-1373. by E. Rivas, R. J. Klein, T. A. Jones, S. R. Eddy posted to computational_biology genes genome rna by marcius on 2006-02-10 20:26:44 as along with 7 people and 4 groups NicholasErho myrtilus evaf eckart_bindewald arcticrasta dquest bsmagic Bioinformatics BioinfoCIPF bioinplant SGU-CIPF
	Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement [My Copy] Protein Engineering, Design and Selection, Vol. 19, No. 2. (February 2006), pp. 55-65. by Wei Zhang, Yong Duan posted to ab-initio algorithms biophysics computational_biology protein_structure structure_prediction by marcius on 2006-01-27 01:13:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	Database-derived potentials dependent on protein size for in silico folding and design. [My Copy] Biophys J, Vol. 87, No. 1. (July 2004), pp. 171-181. by Y. Dehouck, D. Gilis, M. Rooman posted to computational_biology model_assessment by marcius on 2006-01-20 22:59:04 as along with 2 groups BioinfoCIPF SGU-CIPF
	An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields. [My Copy] Biophys J, Vol. 89, No. 5. (November 2005), pp. 3008-3016. by T. Aynechi, I. D. Kuntz posted to bioinformatics biophysics computational_biology model_assessment molecular_dynamics by marcius on 2006-01-20 22:54:26 as along with 1 person and 2 groups nickolay BioinfoCIPF SGU-CIPF
	Simulation of non-specific proteinmRNA interactions [My Copy] Nucleic Acids Research, Vol. 33, No. 21. (2005), pp. 6694-6699. by James Magee, Jim Warwicker posted to biophysics computational_biology molecular_dynamics protein rna by marcius on 2006-01-12 19:13:27 as along with 2 groups BioinfoCIPF SGU-CIPF
	A comprehensive comparison of comparative RNA structure prediction approaches. [My Copy] BMC bioinformatics, Vol. 5, No. 1. (30 September 2004) by Paul P. Gardner, Robert Giegerich posted to bioinformatics computational_biology rna secondary_structure structure by marcius on 2005-12-21 19:13:13 as along with 10 people and 3 groups rb_india agrobledo heliopais evaf austin andersbj arcticrasta penka Hosna Carnegie microRNA BioinfoCIPF SGU-CIPF
	RNA folding: models and perspectives. [My Copy] Curr Opin Struct Biol, Vol. 13, No. 3. (June 2003), pp. 309-316. by T. R. Sosnick, T. Pan posted to biophysics computational_biology folding rna structure by marcius on 2005-12-20 01:07:48 as along with 3 people and 2 groups evaf Hosna austin BioinfoCIPF SGU-CIPF
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to ab-initio biophysics computational_biology structure_prediction by marcius on 2005-11-02 09:16:25 as along with 11 people and 4 groups ucbcjbm paddydu kgutwin BragilMassoud ana barry thaliana jwm vavi gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. [My Copy] J Mol Biol, Vol. 224, No. 3. (5 April 1992), pp. 725-732. by G. Casari, M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:29 as along with 2 groups BioinfoCIPF SGU-CIPF
	Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. [My Copy] J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501. by M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:19 as along with 3 people and 2 groups dgront aengisch mcbla BioinfoCIPF SGU-CIPF
	Knowledge-based potentials for proteins. [My Copy] Curr Opin Struct Biol, Vol. 5, No. 2. (April 1995), pp. 229-235. by M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:08 as along with 4 people and 2 groups chad_davis eckart_bindewald tolot27 janasont BioinfoCIPF SGU-CIPF
	Threading thrills and threats. [My Copy] Structure, Vol. 4, No. 1. (15 January 1996), pp. 15-19. by M. J. Sippl, H. Flöckner posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:18:59 as along with 2 groups BioinfoCIPF SGU-CIPF
	Empirical potentials and functions for protein folding and binding. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 222-228. by S. Vajda, M. Sippl, J. Novotny posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:18:50 as along with 2 people and 2 groups kgutwin chad_davis BioinfoCIPF SGU-CIPF
	Theory and simulation. Old problems, new paradigms. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 179-180. by J. Novotny, M. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:18:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	The role of protein structure in genomics. [My Copy] FEBS Lett, Vol. 476, No. 1-2. (30 June 2000), pp. 98-102. by F. S. Domingues, W. A. Koppensteiner, M. J. Sippl posted to computational_biology review statistical_potentials structural_genomics structure_prediction by marcius on 2005-10-26 19:18:29 as along with 2 groups BioinfoCIPF SGU-CIPF
	Knowledge-based potentials--back to the roots. [My Copy] Biochemistry (Mosc), Vol. 63, No. 3. (March 1998), pp. 247-252. by W. A. Koppensteiner, M. J. Sippl posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:18:16 as along with 1 person and 2 groups tolot27 BioinfoCIPF SGU-CIPF
	Convergent evolution as a mechanism for pathogenic adaptation. [My Copy] Trends Microbiol (7 September 2005) by Sergey Sikora, Alex Strongin, Adam Godzik posted to comparative_modeling computational_biology evolution molecular_mimicry by marcius on 2005-10-26 04:17:30 as along with 1 person and 4 groups ana structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	How do side chains orient globally in protein structures? [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 3. (8 September 2005), pp. 513-522. by Aimin Yan, Robert L. Jernigan posted to classification computational_biology protein_structure side_chains by marcius on 2005-10-23 02:54:16 as along with 2 people and 2 groups aqeel blackbart BioinfoCIPF SGU-CIPF
	Comparative molecular dynamics-Similar folds and similar motions? [My Copy] Proteins (17 October 2005) by Andrew Pang, Yalini Arinaminpathy, Mark S P S. Sansom, Philip C C. Biggin posted to biophysics computational_biology molecular_dynamics protein_structure by marcius on 2005-10-22 16:56:55 as along with 2 people and 2 groups edvin ubcg08l BioinfoCIPF SGU-CIPF
	Hamiltonians for protein tertiary structure prediction based on three-dimensional environment principles. [My Copy] J Mol Biol, Vol. 233, No. 3. (October 1993), pp. 480-487. by T. Madej, M. C. Mossing posted to algorithms computational_biology protein_structure structure_prediction by marcius on 2005-10-22 03:09:41 as along with 2 groups BioinfoCIPF SGU-CIPF
	Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models. [My Copy] Protein Eng Des Sel, Vol. 17, No. 8. (August 2004), pp. 613-624. by T. A. Eyre, L. Partridge, J. M. Thornton posted to computational_biology membrane_protein protein_structure structure_prediction by marcius on 2005-10-22 03:09:41 as along with 2 groups BioinfoCIPF SGU-CIPF
	Recoverable one-dimensional encoding of protein three-dimensional structures. [My Copy] Bioinformatics (February 2005) by Akira R. R. Kinjo, Ken Nishikawa posted to structure_prediction computational_biology protein_structure by marcius on 2005-10-22 03:09:41 as along with 2 groups BioinfoCIPF SGU-CIPF
	LGA: A method for finding 3D similarities in protein structures. [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (July 2003), pp. 3370-3374. by A. Zemla posted to algorithms computational_biology protein_structure structure_prediction by marcius on 2005-10-22 03:09:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	The grail problem. [My Copy] Genome Biol, Vol. 1, No. 1. (2000) by G. A. Petsko posted to computational_biology protein_structure structure_prediction by marcius on 2005-10-22 03:09:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	Model behavior. [My Copy] Genome Biol, Vol. 2, No. 7. (2001) by G. A. Petsko posted to computational_biology protein_structure structure_prediction by marcius on 2005-10-22 03:09:40 as along with 2 groups BioinfoCIPF SGU-CIPF
	The protein structure prediction problem could be solved using the current PDB library. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 1029-1034. by Y. Zhang, J. Skolnick posted to computational_biology evolution protein_folding protein_structure structural_genomics by marcius on 2005-10-21 21:56:14 as along with 14 people and 3 groups Lombardo_7 semin xingwuliu mijam sschurer karbak iakes vavi alexg j3xucite kracher schuylrp jfmuggs neils BioinfoCIPF Immunoinformatics SGU-CIPF
	Scoring function for automated assessment of protein structure template quality [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 4., pp. 702-710. by Yang Zhang, Jeffrey Skolnick posted to computational_biology model_assessment protein_structure by marcius on 2005-10-21 21:55:27 as along with 8 people and 2 groups pjcite saunders reyez karbak dgront aengisch rabio granujilla BioinfoCIPF SGU-CIPF
	Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions. [My Copy] Proteins, Vol. 52, No. 4. (1 September 2003), pp. 492-509. by L. R. Forrest, T. B. Woolf posted to computational_biology model_assessment protein_structure software by marcius on 2005-10-21 21:08:44 as along with 1 person and 2 groups thaliana BioinfoCIPF SGU-CIPF
	Effective energy function for proteins in solution. [My Copy] Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152. by T. Lazaridis, M. Karplus posted to computational_biology model_assessment protein_folding software by marcius on 2005-10-21 21:08:08 as along with 6 people and 2 groups melo_mcr oceanwind bluvsh1 choonpeng hmk kgutwin BioinfoCIPF SGU-CIPF
	Ab initio folding of proteins using restraints derived from evolutionary information. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 177-185. by A. R. Ortiz, A. Kolinski, P. Rotkiewicz, B. Ilkowski, J. Skolnick posted to biophysics computational_biology evolution protein_folding by marcius on 2005-10-21 20:28:33 as along with 1 person and 2 groups gbart BioinfoCIPF SGU-CIPF
	Sequence evolution and the mechanism of protein folding. [My Copy] Biophys J, Vol. 79, No. 4. (October 2000), pp. 1787-1799. by A. R. Ortiz, J. Skolnick posted to biophysics computational_biology evolution protein_structure by marcius on 2005-10-21 20:27:05 as along with 2 people and 2 groups penka cjeans BioinfoCIPF SGU-CIPF
	MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. [My Copy] Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364. by L. Lu, H. Lu, J. Skolnick posted to computational_biology protein_interactions protein_structure by marcius on 2005-10-21 19:36:56 as along with 6 people and 5 groups ana bicko chad_davis sangeetha ruvido kgutwin structural_bioinformatics Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	The PDB is a covering set of small protein structures. [My Copy] Journal of molecular biology, Vol. 334, No. 4. (5 December 2003), pp. 793-802. by Daisuke Kihara, Jeffrey Skolnick posted to computational_biology evolution protein_fragments protein_structure structural_genomics by marcius on 2005-10-21 10:08:41 as along with 3 people and 2 groups gawells iakes j3xucite BioinfoCIPF SGU-CIPF

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rna	213
bioinformatics	196
review	127
biophysics	90
protein_structure	86
structure	86
evolution	86
structure_prediction	64
algorithms	56
computational_biology	53
secondary_structure	53
protein	43
folding	41
classification	38
ncrna	35
casp	35
drug	32
docking	32
protein_interactions	31
genome	30
function	29
microrna	27
cafasp	26
sequence_alignment	25
protein_function	24
software	23
views	22
servers	22
comparative_modeling	19
model_assessment	19
statistical_potentials	19
biology	18
structural_genomics	18
databases	17
ribosome	16
nmr	16
disease	16
protein_domains	15
ligand	15
protein_folding	15
bioengineering	14
clustering	14
protein_fragments	14
ab-initio	12
structure_alignment	11
genes	11
prediction	11
dna	10
statistics	9
snp	9
alignment	9
model_evaluation	8
membrane_protein	7
experimental	7
gene_expression	6
systems_biology	6
microarray	6
phylogeny	6
virus	5
mechano_receptors	5
foce_field	5
sequence	5
protein_threading	5
motif	5
molecular_dynamics	5
text_mining	4
ribozyme	4
discovery	4
rotamers	4
sequence-structure	4
protein_complexes	3
cancer	3
comparative_docking	3
server	3
news	3
human	3
interaction	3
meeting	3
immunology	2
programming	2
hypotesis	2
allosteric	2
proteomics	2
editorial	2
pleiotropy	2
pdb	2
hts	2
trypsin	1
ontology	1
loop_modeling	1
proteases	1
metabolomics	1
opensourcebiology	1
nucleosome	1
side_chains	1
protein_disorder	1
protein_design	1
nanotechnology	1
membrane	1
stability	1
disulfide	1
position	1
web20	1
malaria	1
congress	1
synthetic_biology	1
fold	1
glyco	1
dynamics	1
machine_learning	1
mysql	1
aminoacid_alphabets	1
metagenomics	1
php	1
molecular_mimicry	1
stem_cells	1
consensus	1
plant	1

marcius's computational_biology [53 articles] Export

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