ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn-Munkres Algorithm
暂无分享,去创建一个
Toshiro Kubota | Berhane Temelso | George C. Shields | Joel M. Mabey | Nana Appiah-Padi | Toshiro Kubota | G. Shields | B. Temelso | Nana Appiah-Padi
[1] Chris Morley,et al. Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.
[2] Paola Gratteri,et al. Field interaction and geometrical overlap: a new simplex and experimental design based computational procedure for superposing small ligand molecules. , 2003, Journal of medicinal chemistry.
[3] W. Graham Richards,et al. Ultrafast shape recognition to search compound databases for similar molecular shapes , 2007, J. Comput. Chem..
[4] Paolo Tosco,et al. Open3DALIGN: an open-source software aimed at unsupervised ligand alignment , 2011, J. Comput. Aided Mol. Des..
[5] Ana L. Teixeira,et al. Noncontiguous Atom Matching Structural Similarity Function , 2013, J. Chem. Inf. Model..
[6] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[7] Pavel Hobza,et al. Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field. , 2008, Physical chemistry chemical physics : PCCP.
[8] A. Peter Johnson,et al. An algorithm for the multiple common subgraph problem , 1992, Journal of chemical information and computer sciences.
[9] Karel Berka,et al. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples , 2008 .
[10] Jürgen Bajorath,et al. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. , 2007, Drug discovery today.
[11] K. Dill,et al. Using quaternions to calculate RMSD , 2004, J. Comput. Chem..
[12] Marek Sierka,et al. Similarity recognition of molecular structures by optimal atomic matching and rotational superposition , 2012, J. Comput. Chem..
[13] John M. Barnard,et al. Chemical Similarity Searching , 1998, J. Chem. Inf. Comput. Sci..
[14] W. Kabsch. A solution for the best rotation to relate two sets of vectors , 1976 .
[15] Jordi Mestres,et al. MIMIC: A molecular‐field matching program. Exploiting applicability of molecular similarity approaches , 1997 .
[16] Charles F. F. Karney. Quaternions in molecular modeling. , 2005, Journal of molecular graphics & modelling.
[17] Vladimir Poroikov,et al. Chemical Similarity Assessment through Multilevel Neighborhoods of Atoms: Definition and Comparison with the Other Descriptors , 1999, J. Chem. Inf. Comput. Sci..
[18] William J. Allen,et al. Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design , 2014, J. Chem. Inf. Model..
[19] Xueguang Shao,et al. Structural Distribution of Lennard-Jones Clusters Containing 562 to 1000 Atoms. , 2004, The journal of physical chemistry. A.
[20] R. Glen,et al. Molecular similarity: a key technique in molecular informatics. , 2004, Organic & biomolecular chemistry.
[21] Arne Wagner,et al. aRMSD: A Comprehensive Tool for Structural Analysis , 2017, J. Chem. Inf. Model..
[22] H. Kuhn. The Hungarian method for the assignment problem , 1955 .
[23] Jorge M. C. Marques,et al. How Different Are Two Chemical Structures? , 2010, J. Chem. Inf. Model..
[24] B. Fan,et al. Molecular similarity and diversity in chemoinformatics: From theory to applications , 2006, Molecular Diversity.
[25] Mark S. Johnson,et al. ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential , 2009, J. Chem. Inf. Model..
[26] Michel Petitjean,et al. On the root mean square quantitative chirality and quantitative symmetry measures , 1999 .
[27] Haiyan Jiang,et al. An Efficient Method Based on Lattice Construction and the Genetic Algorithm for Optimization of Large Lennard-Jones Clusters. , 2004, The journal of physical chemistry. A.
[28] Jean-Loup Faulon,et al. Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs , 1998, J. Chem. Inf. Comput. Sci..
[29] G. Shields,et al. Hydration of the sulfuric acid-methylamine complex and implications for aerosol formation. , 2014, The journal of physical chemistry. A.
[30] Patrizia Calaminici,et al. The discovery of unexpected isomers in sodium heptamers by Born-Oppenheimer molecular dynamics. , 2009, The Journal of chemical physics.
[31] M. T. Barakat,et al. Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules , 1990, J. Comput. Aided Mol. Des..
[32] Gert Thijs,et al. Pharao: pharmacophore alignment and optimization. , 2008, Journal of molecular graphics & modelling.
[33] J. A. Grant,et al. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..
[34] J. Doye,et al. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.
[35] Takeshi Kawabata,et al. Build-Up Algorithm for Atomic Correspondence between Chemical Structures , 2011, J. Chem. Inf. Model..
[36] Berhane Temelso,et al. Benchmark structures and binding energies of small water clusters with anharmonicity corrections. , 2011, The journal of physical chemistry. A.
[37] J. Munkres. ALGORITHMS FOR THE ASSIGNMENT AND TRANSIORTATION tROBLEMS* , 1957 .
[38] Thierry Langer,et al. Efficient overlay of small organic molecules using 3D pharmacophores , 2007, J. Comput. Aided Mol. Des..
[39] D. K. Friesen,et al. A combinatorial algorithm for calculating ligand binding , 1984 .
[40] G. Stoltz,et al. Permutation-invariant distance between atomic configurations. , 2015, The Journal of chemical physics.
[41] D R Flower. Rotational superposition: a review of methods. , 1999, Journal of molecular graphics & modelling.
[42] G. Shields,et al. Accurate predictions of water cluster formation, (H₂O)(n=2-10). , 2010, The journal of physical chemistry. A.