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Results: 1 to 20 of 98

1.

Breadth-first search approach to enumeration of tree-like chemical compounds.

Zhao Y, Hayashida M, Jindalertudomdee J, Nagamochi H, Akutsu T.

J Bioinform Comput Biol. 2013 Dec;11(6):1343007. doi: 10.1142/S0219720013430075. Epub 2013 Nov 21.

PMID:
24372036
[PubMed - in process]
2.

Efficient enumeration of monocyclic chemical graphs with given path frequencies.

Suzuki M, Nagamochi H, Akutsu T.

J Cheminform. 2014 May 30;6:31. doi: 10.1186/1758-2946-6-31. eCollection 2014.

PMID:
24955135
[PubMed]
Free PMC Article
3.

Improved algorithms for enumerating tree-like chemical graphs with given path frequency.

Ishida Y, Zhao L, Nagamochi H, Akutsu T.

Genome Inform. 2008;21:53-64.

PMID:
19425147
[PubMed - indexed for MEDLINE]
Free Article
4.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
[PubMed - as supplied by publisher]
5.

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming.

Imada T, Ota S, Nagamochi H, Akutsu T.

J Chem Inf Model. 2011 Nov 28;51(11):2788-807. doi: 10.1021/ci200084b. Epub 2011 Oct 25.

PMID:
21848281
[PubMed - indexed for MEDLINE]
6.

Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies.

Shimizu M, Nagamochi H, Akutsu T.

BMC Bioinformatics. 2011 Dec 14;12 Suppl 14:S3. doi: 10.1186/1471-2105-12-S14-S3.

PMID:
22373441
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Computing paths and cycles in biological interaction graphs.

Klamt S, von Kamp A.

BMC Bioinformatics. 2009 Jun 15;10:181. doi: 10.1186/1471-2105-10-181.

PMID:
19527491
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Designing an A* algorithm for calculating edit distance between rooted-unordered trees.

Horesh Y, Mehr R, Unger R.

J Comput Biol. 2006 Jul-Aug;13(6):1165-76.

PMID:
16901235
[PubMed - indexed for MEDLINE]
9.

Enumerating treelike chemical graphs with given path frequency.

Fujiwara H, Wang J, Zhao L, Nagamochi H, Akutsu T.

J Chem Inf Model. 2008 Jul;48(7):1345-57. doi: 10.1021/ci700385a. Epub 2008 Jun 28.

PMID:
18588284
[PubMed]
10.

LEAP into the Pfizer Global Virtual Library (PGVL) space: creation of readily synthesizable design ideas automatically.

Hu Q, Peng Z, Kostrowicki J, Kuki A.

Methods Mol Biol. 2011;685:253-76. doi: 10.1007/978-1-60761-931-4_13.

PMID:
20981528
[PubMed - indexed for MEDLINE]
11.

[Development of antituberculous drugs: current status and future prospects].

Tomioka H, Namba K.

Kekkaku. 2006 Dec;81(12):753-74. Review. Japanese.

PMID:
17240921
[PubMed - indexed for MEDLINE]
12.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

Hafner J.

J Phys Condens Matter. 2008 Feb 13;20(6):060301. doi: 10.1088/0953-8984/20/06/060301. Epub 2008 Jan 24.

PMID:
21693862
[PubMed]
13.

Triplet supertree heuristics for the tree of life.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S8. doi: 10.1186/1471-2105-10-S1-S8.

PMID:
19208181
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Estimation of the size of drug-like chemical space based on GDB-17 data.

Polishchuk PG, Madzhidov TI, Varnek A.

J Comput Aided Mol Des. 2013 Aug;27(8):675-9. doi: 10.1007/s10822-013-9672-4. Epub 2013 Aug 21.

PMID:
23963658
[PubMed - indexed for MEDLINE]
15.

Efficient extraction of mapping rules of atoms from enzymatic reaction data.

Akutsu T.

J Comput Biol. 2004;11(2-3):449-62.

PMID:
15285901
[PubMed - indexed for MEDLINE]
16.

Ligand-based virtual screening and in silico design of new antimalarial compounds using nonstochastic and stochastic total and atom-type quadratic maps.

Marrero-Ponce Y, Iyarreta-Veitía M, Montero-Torres A, Romero-Zaldivar C, Brandt CA, Avila PE, Kirchgatter K, Machado Y.

J Chem Inf Model. 2005 Jul-Aug;45(4):1082-100.

PMID:
16045304
[PubMed - indexed for MEDLINE]
17.

A Condition-Enumeration Tree method for mining biclusters from DNA microarray data sets.

Chen JR, Chang YI.

Biosystems. 2009 Jul;97(1):44-59. doi: 10.1016/j.biosystems.2009.04.003. Epub 2009 Apr 23.

PMID:
19393714
[PubMed - indexed for MEDLINE]
18.

Application of kernel functions for accurate similarity search in large chemical databases.

Wang X, Huan J, Smalter A, Lushington GH.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S8. doi: 10.1186/1471-2105-11-S3-S8.

PMID:
20438655
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Characterizing the phylogenetic tree-search problem.

Money D, Whelan S.

Syst Biol. 2012 Mar;61(2):228-39. doi: 10.1093/sysbio/syr097. Epub 2011 Nov 10.

PMID:
22076302
[PubMed - indexed for MEDLINE]
20.

How evolutionary crystal structure prediction works--and why.

Oganov AR, Lyakhov AO, Valle M.

Acc Chem Res. 2011 Mar 15;44(3):227-37. doi: 10.1021/ar1001318. Epub 2011 Mar 1.

PMID:
21361336
[PubMed]

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