ca3295's library 67 articles Export

	Rational design of peptide-based building blocks for nanoscience and synthetic biology [My Copy] Faraday Discuss., Vol. 143 (2009), pp. 305-317. by Craig T. Armstrong, Aimee L. Boyle, Elizabeth H. C. Bromley, et al.Zahra N. Mahmoud, Lisa Smith, Andrew R. Thomson, Derek N. Woolfson posted to synthetic pcomp biology by ca3295 on 2009-11-13 13:54:02 as along with 1 person samjlord
	Lessons from zinc-binding peptides. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 26 (1997), pp. 357-371. by J. M. Berg, H. A. Godwin posted to binding finger metal review zinc by ca3295 on 2008-05-27 18:01:23 as
	Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 24. (13 June 2006), pp. 8989-8994. by J. M. Mason, M. A. Schmitz, K. M. Müller, K. M. Arndt posted to coiled-coil dimerization hetero by ca3295 on 2008-05-27 16:57:06 as along with 4 people kgutwin gwenknight chgjb bethbromley
	Structure-based prediction of bZIP partnering specificity. [My Copy] J Mol Biol, Vol. 355, No. 5. (3 February 2006), pp. 1125-1142. by G. Grigoryan, A. E. Keating posted to coiled-coil dimerization hetero paterner selection by ca3295 on 2008-05-27 16:55:16 as along with 4 people cjeans hplatero gwenknight chgjb
	Architectural rules of the zinc-finger motif: comparative two-dimensional NMR studies of native and "aromatic-swap" domains define a "weakly polar switch". [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 88, No. 19. (1 October 1991), pp. 8455-8459. by M. Kochoyan, H. T. Keutmann, M. A. Weiss posted to core finger hydrophobic switch zinc by ca3295 on 2008-05-27 15:14:14 as
	Similarity of phylogenetic trees as indicator of protein-protein interaction [My Copy] Protein Eng., Vol. 14, No. 9. (1 September 2001), pp. 609-614. by Florencio Pazos, Alfonso Valencia posted to covariance by ca3295 on 2008-05-27 15:10:37 as along with 8 people jperkins Robinder marti balajis IbnBio tale selrac bicko
	Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation [My Copy] Algorithms for Molecular Biology, Vol. 2 (03 October 2007), 12. by Rodrigo Gouveia-Oliveira, Anders G. Pedersen posted to covariance by ca3295 on 2008-05-27 15:08:56 as along with 3 people bicko nklee IrinaMoreira
	An integrated system for studying residue coevolution in proteins [My Copy] Bioinformatics, Vol. 24, No. 2. (15 January 2008), pp. 290-292. by Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew Mcdermott, Mark Gerstein posted to covariance by ca3295 on 2008-05-27 15:06:04 as along with 6 people and 1 group leemond31 qluo marck sobolevnrm chrys friendpine baker-group
	A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 10. (10 July 2004), pp. 1565-1572. by John P. Dekker, Anthony Fodor, Richard W. Aldrich, Gary Yellen posted to covariance by ca3295 on 2008-05-27 15:05:16 as along with 5 people mgomes qluo gbart Haggan cjeans
	Evolutionarily conserved networks of residues mediate allosteric communication in proteins [My Copy] Nature Structural & Molecular Biology, Vol. 10, No. 1. (16 December 2002), pp. 59-69. by Gurol M. Suel, Steve W. Lockless, Mark A. Wall, Rama Ranganathan posted to covariance sca by ca3295 on 2008-05-27 15:02:59 as along with 20 people and 3 groups mgomes qluo arjun_citeulike RebeccaHamer ynaito lna dimka marcius eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum biomedical-nlp BioinfoCIPF SGU-CIPF
	On Evolutionary Conservation of Thermodynamic Coupling in Proteins [My Copy] Journal of Biological Chemistry, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050. by A. A. Fodor, R. W. Aldrich posted to coupling covariance by ca3295 on 2008-05-27 14:56:48 as along with 7 people and 2 groups ana barry gbart cjeans tale friendpine Lombardo_7 structural_bioinformatics Bioinformatics
	Pfam: a comprehensive database of protein domain families based on seed alignments. [My Copy] Proteins, Vol. 28, No. 3. (July 1997), pp. 405-420. by E. L. Sonnhammer, S. R. Eddy, R. Durbin posted to database hmm pfam by ca3295 on 2008-05-27 14:52:18 as along with 7 people and 1 group thegoose2 tharris pcahan1 cjeans antonkratz marti gulkur C. elegans / WormBase
	Predicting coiled coils from protein sequences. [My Copy] Science (New York, N.Y.), Vol. 252, No. 5010. (24 May 1991), pp. 1162-1164. by A. Lupas, M. Van Dyke, J. Stock posted to coiled-coil prediction by ca3295 on 2008-05-27 14:42:42 as along with 3 people TLVincent kgutwin gwenknight
	An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. [My Copy] Bioinformatics (Oxford, England), Vol. 18, No. 4. (April 2002), pp. 617-625. by Mauro Delorenzi, Terry Speed posted to coiled-coil hmm prediction by ca3295 on 2008-05-27 14:41:30 as along with 6 people TLVincent kgutwin oteri hansen cjeans gwenknight
	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 to coiled-coil prediction review by ca3295 on 2008-05-27 14:40:34 as along with 5 people and 1 group TLVincent kgutwin oteri cjeans marck Structural Biology Group TorVergata
	MultiCoil: a program for predicting two- and three-stranded coiled coils. [My Copy] Protein science : a publication of the Protein Society, Vol. 6, No. 6. (June 1997), pp. 1179-1189. by E. Wolf, P. S. Kim, B. Berger posted to oligomerization paircoil prediction state by ca3295 on 2008-05-27 14:39:10 as along with 3 people and 1 group TLVincent oteri kgutwin Structural Biology Group TorVergata
	N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. [My Copy] Protein Sci, Vol. 4, No. 7. (July 1995), pp. 1325-1336. by A. J. Doig, R. L. Baldwin posted to capping helix by ca3295 on 2008-05-27 14:35:49 as along with 1 person bethbromley
	Helix capping interactions stabilize the N-terminus of the kinesin neck coiled-coil. [My Copy] Journal of structural biology, Vol. 137, No. 1-2. (b 2002), pp. 220-235. by B. Tripet, R. S. Hodges posted to alanine capping d position by ca3295 on 2008-05-27 14:35:21 as
	Predicting oligomerization states of coiled coils. [My Copy] Protein science : a publication of the Protein Society, Vol. 4, No. 8. (August 1995), pp. 1596-1607. by D. N. Woolfson, T. Alber posted to co coiled-coil oligomerization scorer state by ca3295 on 2008-05-27 14:30:48 as along with 4 people TLVincent Lombardo_7 kgutwin marck
	Hydrolytic reaction by zinc finger mutant peptides: successful redesign of structural zinc sites into catalytic zinc sites. [My Copy] Inorganic chemistry, Vol. 43, No. 5. (8 March 2004), pp. 1708-1713. by A. Nomura, Y. Sugiura posted to binding deletion finger ligand metal zinc by ca3295 on 2008-05-27 14:29:20 as
	Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. [My Copy] Journal of biomolecular NMR, Vol. 2, No. 6. (November 1992), pp. 661-665. by M. Piotto, V. Saudek, V. Sklenár posted to nmr solvent supression watergate by ca3295 on 2008-05-27 14:27:52 as
	Metal binding properties of single amino acid deletion mutants of zinc finger peptides: studies using cobalt(II) as a spectroscopic probe. [My Copy] Biophysical journal, Vol. 64, No. 3. (March 1993), pp. 749-753. by Y. Shi, R. D. Beger, J. M. Berg posted to binding finger metal zinc by ca3295 on 2008-05-27 14:26:32 as
	Metal-dependent folding of a single zinc finger from transcription factor IIIA. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 84, No. 14. (July 1987), pp. 4841-4845. by A. D. Frankel, J. M. Berg, C. O. Pabo posted to binding circular dichroism finger metal zinc by ca3295 on 2008-05-27 14:23:18 as
	Effects of side-chain characteristics on stability and oligomerization state of a de Novo-designed model coiled-coil: 20 amino acid substitutions in position “d”1 [My Copy] Journal of Molecular Biology, Vol. 300, No. 2. (07 July 2000), pp. 377-402. by B. Tripet, K. Wagschal, P. Lavigne, C. T. Mant, R. S. Hodges posted to coiled-coil d position stability by ca3295 on 2008-05-27 14:21:40 as along with 3 people dr_proton cjeans hplatero
	Establishing homologies in protein sequences. [My Copy] Methods Enzymol, Vol. 91 (1983), pp. 524-545. by M. O. Dayhoff, W. C. Barker, L. T. Hunt posted to matrix pam substitution by ca3295 on 2008-05-27 14:15:15 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Using substitution probabilities to improve position-specific scoring matrices. [My Copy] Computer applications in the biosciences : CABIOS, Vol. 12, No. 2. (April 1996), pp. 135-143. by J. G. Henikoff, S. Henikoff posted to counts pseudo by ca3295 on 2008-05-27 14:12:35 as along with 1 person maria_hauser
	Socket: a program for identifying and analysing coiled-coil motifs within protein structures. [My Copy] Journal of molecular biology, Vol. 307, No. 5. (13 April 2001), pp. 1427-1450. by J. Walshaw, D. N. Woolfson posted to cc coiled-coil database socket by ca3295 on 2008-05-27 14:10:32 as along with 5 people TLVincent oteri kgutwin martainn gbartbristol
	Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds. [My Copy] J Am Chem Soc, Vol. 128, No. 4. (1 February 2006), pp. 1154-1161. by X. I. Ambroggio, B. Kuhlman posted to coiled-coil finger sw1 switch zinc by ca3295 on 2008-05-27 14:08:27 as along with 5 people and 2 groups barry shuns jwm kevinchannon bethbromley structural_bioinformatics Bioinformatics
	ZiCo: a peptide designed to switch folded state upon binding zinc. [My Copy] J Am Chem Soc, Vol. 127, No. 43. (2 November 2005), pp. 15008-15009. by E. Cerasoli, B. K. Sharpe, D. N. Woolfson posted to coiled-coil finger switch zico zinc by ca3295 on 2008-05-27 14:07:18 as along with 3 people patrickking kevinchannon bethbromley
	Sequence and structural duality: designing peptides to adopt two stable conformations. [My Copy] J Am Chem Soc, Vol. 126, No. 51. (29 December 2004), pp. 17016-17024. by M. J. Pandya, E. Cerasoli, A. Joseph, R. G. Stoneman, E. Waite, D. N. Woolfson posted to coiled-coil hairpin switch by ca3295 on 2008-05-27 14:06:14 as along with 1 person bethbromley
	Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. [My Copy] Biochemistry, Vol. 13, No. 2. (15 January 1974), pp. 211-222. by P. Y. Chou, G. D. Fasman posted to propensities secondary structure by ca3295 on 2008-05-27 14:04:55 as along with 1 person kgutwin
	A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins. [My Copy] J Biol Chem, Vol. 277, No. 12. (22 March 2002), pp. 10150-10155. by B. Ciani, E. G. Hutchinson, R. B. Sessions, D. N. Woolfson posted to alpha beta discordant switch by ca3295 on 2008-05-27 14:03:21 as along with 2 people kevinchannon bethbromley
	Structure and dynamics of molecular motors. [My Copy] Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 239-246. by L. A. Amos, R. A. Cross posted to actin molecular motors myosin review by ca3295 on 2008-05-27 14:01:25 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to design threading top7 by ca3295 on 2008-05-27 13:56:40 as along with 10 people bmduggan kgutwin Diego_Prada onufriev apaydin dfgreen jwm hmk heymiki kevinchannon
	Structural test of the parameterized-backbone method for protein design. [My Copy] Journal of molecular biology, Vol. 342, No. 1. (3 September 2004), pp. 289-297. by J. J. Plecs, P. B. Harbury, P. S. Kim, T. Alber posted to coiled-coil handed right by ca3295 on 2008-05-27 13:55:41 as along with 1 person kgutwin
	Electrostatic Control of Thickness and Stiffness in a Designed Protein Fiber [My Copy] J. Am. Chem. Soc. (25 March 2008) by David Papapostolou, Elizabeth H. Bromley, Christopher Bano, Derek N. Woolfson posted to assembly safs self by ca3295 on 2008-05-27 13:54:31 as along with 2 people and 1 group patrickking evan2008 KeatingJClub
	Sticky-end assembly of a designed peptide fiber provides insight into protein fibrillogenesis. [My Copy] Biochemistry, Vol. 39, No. 30. (1 August 2000), pp. 8728-8734. by M. J. Pandya, G. M. Spooner, M. Sunde, J. R. Thorpe, A. Rodger, D. N. Woolfson posted to assembly safs self by ca3295 on 2008-05-27 13:53:30 as
	Ab initio protein structure prediction of CASP III targets using ROSETTA. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 171-176. by K. T. Simons, R. Bonneau, I. Ruczinski, D. Baker posted to rosetta by ca3295 on 2008-05-27 13:46:18 as
	Biological sequence analysis. Probablistic models of proteins and nucleic acids [My Copy] (1998) by R. Durbin, S. Eddy, A. Krogh, G. Mitchison posted to analysis book hmm sequence by ca3295 on 2008-05-27 13:40:39 as
	The HHpred interactive server for protein homology detection and structure prediction. [My Copy] Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005) by J. Söding, A. Biegert, A. N. Lupas posted to hhpred hmm by ca3295 on 2008-05-27 13:28:03 as along with 2 people grottenolm granujilla
	Profile hidden Markov models [My Copy] Bioinformatics, Vol. 14, No. 9. (1 October 1998), pp. 755-763. by S. R. Eddy posted to hidden hmm markov model profile review by ca3295 on 2008-05-27 13:26:14 as along with 14 people ldiambra farhat BioNica druvus albert_swart miguel chad_davis eweaver dgront rabio cjeans suizan nklee yoanjacquemin
	Profile analysis: detection of distantly related proteins. [My Copy] Proc Natl Acad Sci U S A, Vol. 84, No. 13. (July 1987), pp. 4355-4358. by M. Gribskov, A. D. McLachlan, D. Eisenberg posted to profile pssm by ca3295 on 2008-05-27 13:22:43 as along with 3 people dgront rabio Evangelia
	Database of homology-derived protein structures and the structural meaning of sequence alignment. [My Copy] Proteins, Vol. 9, No. 1. (1991), pp. 56-68. by C. Sander, R. Schneider posted to homology sequence structure by ca3295 on 2008-05-27 13:21:12 as along with 2 people chad_davis Lombardo_7
	Ab initio protein fold prediction using evolutionary algorithms: influence of design and control parameters on performance. [My Copy] Journal of computational chemistry, Vol. 27, No. 11. (August 2006), pp. 1177-1195. by D. P. Djurdjevic, M. J. Biggs posted to ab folding initio protein by ca3295 on 2008-05-27 13:16:06 as along with 1 person flbarroso
	Protein-structure prediction by recombination of fragments. [My Copy] Chembiochem, Vol. 7, No. 1. (January 2006), pp. 19-27. by J. M. Bujnicki posted to bioinformatics fragmets prediction by ca3295 on 2008-05-27 12:33:05 as along with 1 person vavi
	Metal binding and folding properties of a minimalist Cys2His2 zinc finger peptide. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 89, No. 11. (1 June 1992), pp. 4796-4800. by S. F. Michael, V. J. Kilfoil, M. H. Schmidt, B. T. Amann, J. M. Berg posted to finger minimalist zinc by ca3295 on 2008-05-27 12:26:45 as
	A CONSENSUS ZINC FINGER PEPTIDE - DESIGN, HIGH-AFFINITY METAL-BINDING, A PH-DEPENDENT STRUCTURE, AND A HIS TO CYS SEQUENCE VARIANT [My Copy] JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol. 113, No. 12. (June 1991), pp. 4518-4523. by B. A. Krizek, B. T. Amann, V. J. Kilfoil, D. L. Merkle, J. M. Berg posted to consensus finger zinc by ca3295 on 2008-05-27 12:25:45 as
	Designer zinc-finger proteins and their applications. [My Copy] Gene, Vol. 366, No. 1. (17 January 2006), pp. 27-38. by M. Papworth, P. Kolasinska, M. Minczuk posted to binding dna finger zinc by ca3295 on 2008-05-27 11:56:36 as along with 1 person aalibes
	Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. [My Copy] Biochemistry, Vol. 41, No. 22. (4 June 2002), pp. 7074-7081. by T. Sera, C. Uranga posted to binding dna finger zinc by ca3295 on 2008-05-27 11:54:30 as
	DNA recognition by Cys2His2 zinc finger proteins. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 29 (2000), pp. 183-212. by S. A. Wolfe, L. Nekludova, C. O. Pabo posted to binding dna finger zinc by ca3295 on 2008-05-27 11:53:22 as along with 1 person kristallreiner

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review	9
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