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CRANKITE: A fast polypeptide backbone conformation sampler.

Podtelezhnikov AA, Wild DL.

Source Code Biol Med. 2008 Jun 24;3:12.PMID: 18577227 [PubMed - in process]Related articlesFree article

Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds.

Podtelezhnikov AA, Wild DL.

Proteins. 2005 Oct 1;61(1):94-104.PMID: 16049911 [PubMed - indexed for MEDLINE]Related articles

Efficient Monte Carlo trial moves for polypeptide simulations.

Betancourt MR.

J Chem Phys. 2005 Nov 1;123(17):174905.PMID: 16375567 [PubMed - indexed for MEDLINE]Related articles

Conformational memories with variable bond angles.

Whitnell RM, Hurst DP, Reggio PH, Guarnieri F.

J Comput Chem. 2008 Apr 15;29(5):741-52.PMID: 17876759 [PubMed - indexed for MEDLINE]Related articles

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space.

Kitao A, Hayward S, Go N.

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Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field.

Cao Z, Lin Z, Wang J, Liu H.

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Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping.

Frickenhaus S, Kannan S, Zacharias M.

J Comput Chem. 2009 Feb;30(3):479-92.PMID: 18680215 [PubMed - indexed for MEDLINE]Related articles

On updating torsion angles of molecular conformations.

Choi V.

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Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces.

Ikeda K, Hirokawa T, Higo J, Tomii K.

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A probabilistic model of RNA conformational space.

Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T.

PLoS Comput Biol. 2009 Jun;5(6):e1000406. Epub 2009 Jun 19.PMID: 19543381 [PubMed - indexed for MEDLINE]Related articlesFree article

Algorithm for backrub motions in protein design.

Georgiev I, Keedy D, Richardson JS, Richardson DC, Donald BR.

Bioinformatics. 2008 Jul 1;24(13):i196-204.PMID: 18586714 [PubMed - indexed for MEDLINE]Related articlesFree article

Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field.

Cui M, Mezei M, Osman R.

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MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space.

Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO.

Eur J Med Chem. 2009 Apr;44(4):1405-9. Epub 2008 Oct 21.PMID: 19022539 [PubMed - indexed for MEDLINE]Related articles

DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins.

Nishima W, Qi G, Hayward S, Kitao A.

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Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design.

Vasudev PG, Chatterjee S, Shamala N, Balaram P.

Acc Chem Res. 2009 Oct 20;42(10):1628-39.PMID: 19572698 [PubMed - in process]Related articles

Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

Okumura H.

J Chem Phys. 2008 Sep 28;129(12):124116.PMID: 19045015 [PubMed - indexed for MEDLINE]Related articles

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

Staneva I, Wallin S.

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The SAAP force field: development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides.

Iwaoka M, Kimura N, Yosida D, Minezaki T.

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Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

Liu X, Bai F, Ouyang S, Wang X, Li H, Jiang H.

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Quantitative description of backbone conformational sampling of unfolded proteins at amino acid resolution from NMR residual dipolar couplings.

Nodet G, Salmon L, Ozenne V, Meier S, Jensen MR, Blackledge M.

J Am Chem Soc. 2009 Dec 16;131(49):17908-18.PMID: 19908838 [PubMed - in process]Related articles