PubMed

Stochastic reconstruction of protein structures from effective connectivity profiles.

Wolff K, Vendruscolo M, Porto M.

PMC Biophys. 2008 Nov 26;1(1):5.PMID: 19351427 [PubMed - in process]Related articlesFree article

A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles.

Wolff K, Vendruscolo M, Porto M.

Gene. 2008 Oct 1;422(1-2):47-51. Epub 2008 Jun 6.PMID: 18577428 [PubMed - indexed for MEDLINE]Related articles

Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences.

Bastolla U, Ortíz AR, Porto M, Teichert F.

Proteins. 2008 Dec;73(4):872-88.PMID: 18536008 [PubMed - indexed for MEDLINE]Related articles

Recovery of protein structure from contact maps.

Vendruscolo M, Kussell E, Domany E.

Fold Des. 1997;2(5):295-306.PMID: 9377713 [PubMed - indexed for MEDLINE]Related articles

Reconstructing protein structure from solvent exposure using tabu search.

Paluszewski M, Hamelryck T, Winter P.

Algorithms Mol Biol. 2006 Oct 27;1:20.PMID: 17069644 [PubMed]Related articlesFree article

Guiding conformation space search with an all-atom energy potential.

Brunette TJ, Brock O.

Proteins. 2008 Dec;73(4):958-72.PMID: 18536015 [PubMed - indexed for MEDLINE]Related articlesFree article

All-atom Monte Carlo approach to protein-peptide binding.

Staneva I, Wallin S.

J Mol Biol. 2009 Nov 13;393(5):1118-28. Epub 2009 Sep 3.PMID: 19733177 [PubMed - indexed for MEDLINE]Related articles

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

Lätzer J, Shen T, Wolynes PG.

Biochemistry. 2008 Feb 19;47(7):2110-22. Epub 2008 Jan 17.PMID: 18198897 [PubMed - indexed for MEDLINE]Related articles

A computational pathway for bracketing native-like structures fo small alpha helical globular proteins.

Narang P, Bhushan K, Bose S, Jayaram B.

Phys Chem Chem Phys. 2005 Jun 7;7(11):2364-75.PMID: 19785123 [PubMed - indexed for MEDLINE]Related articles

Effective knowledge-based potentials.

Ferrada E, Melo F.

Protein Sci. 2009 Jul;18(7):1469-85.PMID: 19530247 [PubMed - indexed for MEDLINE]Related articles

Explicit orientation dependence in empirical potentials and its significance to side-chain modeling.

Ma J.

Acc Chem Res. 2009 Aug 18;42(8):1087-96.PMID: 19445451 [PubMed - indexed for MEDLINE]Related articles

Amino acid interaction preferences in proteins.

Jha AN, Vishveshwara S, Banavar JR.

Protein Sci. 2010 Mar;19(3):603-16.PMID: 20073083 [PubMed - in process]Related articles

Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies.

Sun W, He J.

Proteins. 2009 Oct;77(1):159-73.PMID: 19415754 [PubMed - indexed for MEDLINE]Related articles

Stochastic dynamics of model proteins on a directed graph.

Bongini L, Casetti L, Livi R, Politi A, Torcini A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jun;79(6 Pt 1):061925. Epub 2009 Jun 30.PMID: 19658542 [PubMed - indexed for MEDLINE]Related articles

Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

Li J, Zhu X, Chen JY.

PLoS Comput Biol. 2009 Jul;5(7):e1000450. Epub 2009 Jul 31.PMID: 19649302 [PubMed - indexed for MEDLINE]Related articlesFree article

Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints.

Lin M, Lu HM, Chen R, Liang J.

J Chem Phys. 2008 Sep 7;129(9):094101.PMID: 19044859 [PubMed - indexed for MEDLINE]Related articlesFree article

An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins.

Vadivel K, Namasivayam G.

PLoS One. 2009;4(4):e5148. Epub 2009 Apr 9.PMID: 19357778 [PubMed - indexed for MEDLINE]Related articlesFree article

Dynamics in the metabasin space of a Lennard-Jones glass former: connectivity and transition rates.

Yang Y, Chakraborty B.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jul;80(1 Pt 1):011501. Epub 2009 Jul 15.PMID: 19658707 [PubMed]Related articles

Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins.

Zhuravlev PI, Materese CK, Papoian GA.

J Phys Chem B. 2009 Jul 2;113(26):8800-12.PMID: 19453123 [PubMed - indexed for MEDLINE]Related articles

Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation.

Zhang J, Dundas J, Lin M, Chen R, Wang W, Liang J.

RNA. 2009 Dec;15(12):2248-63. Epub 2009 Oct 28.PMID: 19864433 [PubMed - indexed for MEDLINE]Related articles