Publications
230 results found
Berthold MR, Diederichs K, Glen R, et al., 2005, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface, ISBN: 9783540291046
Bender A, Mussa HY, Glen RC, 2005, Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naive Bayesian classifier: Limitations of the descriptor and the importance of balanced chemistry in training and test sets, JOURNAL OF BIOMOLECULAR SCREENING, Vol: 10, Pages: 658-666, ISSN: 1087-0571
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- Citations: 26
Karthikeyan M, Glen RC, Bender A, 2005, General melting point prediction based on a diverse compound data set and artificial neural networks, JOURNAL OF CHEMICAL INFORMATION AND MODELING, Vol: 45, Pages: 581-590, ISSN: 1549-9596
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- Citations: 95
Bender A, Glen RC, 2005, A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication., J Chem Inf Model, Vol: 45, Pages: 1369-1375, ISSN: 1549-9596
We have performed virtual screening using some very simple features, by employing the number of atoms per element as molecular descriptors but without regard to any structural information whatsoever. Surprisingly, these atom counts are able to outperform virtual-affinity-based fingerprints and Unity fingerprints in some activity classes. Although molecular weight and other biases were known in target-based virtual screening settings (docking), we report the effect of using very simple descriptors for ligand-based virtual screening, by using clearly defined biological targets and employing a large data set (>100,000 compounds) containing multiple (11) activity classes. Structure-unaware atom count vectors as descriptors in combination with the Euclidean distance measure are able to achieve "enrichment factors" over random selection of around 4 (depending on the particular class of active compounds), putting the enrichment factors reported for more sophisticated virtual screening methods in a different light. They are also able to retrieve active compounds with novel scaffolds instead of merely the expected structural analogues. The added value of many currently used virtual screening methods (calculated as enrichment factors) drops down to a factor of between 1 and 2, instead of often reported double-digit figures. The observed effect is much less profound for simple descriptors such as molecular weight and is only present in cases of atypical (larger) ligands. The current state of virtual screening is not as sophisticated as might be expected, which is due to descriptors still not being able to capture structural properties relevant to binding. This fact can partly be explained by highly nonlinear structure-activity relationships, which represent a severe limitation of the "similar property principle" in the context of bioactivity.
Bender A, Klamt A, Wichmann K, et al., 2005, Molecular similarity searching using COSMO screening charges (COSMO/3PP), 1st International Symposium on Computational Life Sciences, Publisher: SPRINGER-VERLAG BERLIN, Pages: 175-185, ISSN: 0302-9743
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- Citations: 2
Nerukh D, Karvounis G, Glen RC, 2004, Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems, COMPLEXITY, Vol: 10, Pages: 40-46, ISSN: 1076-2787
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- Citations: 5
Bender A, Mussa HY, Gill GS, et al., 2004, Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D), JOURNAL OF MEDICINAL CHEMISTRY, Vol: 47, Pages: 6569-6583, ISSN: 0022-2623
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- Citations: 47
Glen RC, 2004, New horizons in molecular informatics., Org Biomol Chem, Vol: 2, Pages: E5-E6, ISSN: 1477-0520
Glen RC, 2004, Future direction of bioinformatics in systems biology, BTS 2004 Annual Congress, Publisher: ELSEVIER SCI IRELAND LTD, Pages: 43-43, ISSN: 0300-483X
Karvounis G, Nerukh D, Glen RC, 2004, Water network dynamics at the critical moment of a peptide's β-turn formation:: A molecular dynamics study, JOURNAL OF CHEMICAL PHYSICS, Vol: 121, Pages: 4925-4935, ISSN: 0021-9606
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- Citations: 16
Bender A, Mussa HY, Glen RC, et al., 2004, Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 44, Pages: 1708-1718, ISSN: 0095-2338
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- Citations: 289
Moloney GP, Garavelas A, Martin G, et al., 2004, Synthesis and serotonergic activity of variously substituted (3-amido)phenylpiperazine derivatives and benzothiophene-4-piperazine derivatives:: novel antagonists for the vascular 5-HT<sub>1B</sub> receptor, EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, Vol: 39, Pages: 305-321, ISSN: 0223-5234
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- Citations: 12
Bender A, Reiling S, Mussa HY, et al., 2004, Similarity searching using atom environments, information gain based feature selection and the naive Bayesian classifier., 227th National Meeting of the American-Chemical Society, Publisher: AMER CHEMICAL SOC, Pages: U907-U907, ISSN: 0065-7727
Zhang Y, Glen RC, Murray-Rust P, et al., 2004, Semantic grid computing - The WorldWideMolecularMatrix., 227th National Meeting of the American-Chemical Society, Publisher: AMER CHEMICAL SOC, Pages: U682-U682, ISSN: 0065-7727
Puvanendrampillai D, Marsden PM, Mitchell JBO, et al., 2004, Comparative evaluation of five scoring functions for accurate prediction of protein-ligand binding energy., 227th National Meeting of the American-Chemical Society, Publisher: AMER CHEMICAL SOC, Pages: U1018-U1018, ISSN: 0065-7727
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- Citations: 1
Bender A, Glen RC, 2004, Molecular similarity: a key technique in molecular informatics, ORGANIC & BIOMOLECULAR CHEMISTRY, Vol: 2, Pages: 3204-3218, ISSN: 1477-0520
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- Citations: 451
Marsden PM, Puvanendrampillai D, Mitchell JBO, et al., 2004, Predicting protein-ligand binding affinities: a low scoring game?, ORGANIC & BIOMOLECULAR CHEMISTRY, Vol: 2, Pages: 3267-3273, ISSN: 1477-0520
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- Citations: 45
Bender A, Mussa HY, Gill GS, et al., 2004, Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT), IEEE International Conference on Systems, Man and Cybernetics, Publisher: IEEE, Pages: 4553-4558, ISSN: 1062-922X
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- Citations: 1
Bender A, Mussa HY, Glen RC, et al., 2003, Molecular similarity searching using atom environments, information-based feature selection, and a naive Bayesian classifier, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 44, Pages: 170-178, ISSN: 0095-2338
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- Citations: 236
Glen RC, Allen SC, 2003, Ligand-protein docking: Cancer research at the interface between biology and chemistry, CURRENT MEDICINAL CHEMISTRY, Vol: 10, Pages: 763-777, ISSN: 0929-8673
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- Citations: 43
Xing L, Glen RC, Clark RD, 2003, Predicting p<i>K</i><sub>a</sub> by molecular tree structured fingerprints and PLS, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 43, Pages: 870-879, ISSN: 0095-2338
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- Citations: 57
Glen R, 2002, Developing tools and standards in molecular informatics. Interview by Susan Aldridge., Chem Commun (Camb), Pages: 2745-2747, ISSN: 1359-7345
Nerukh D, Karvounis G, Glen RC, 2002, Complexity of classical dynamics of molecular systems. I. Methodology, JOURNAL OF CHEMICAL PHYSICS, Vol: 117, Pages: 9611-9617, ISSN: 0021-9606
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- Citations: 17
Nerukh D, Karvounis G, Glen RC, 2002, Complexity of classical dynamics of molecular systems.: II.: Finite statistical complexity of a water-Na<SUP>+</SUP> system, JOURNAL OF CHEMICAL PHYSICS, Vol: 117, Pages: 9618-9622, ISSN: 0021-9606
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- Citations: 6
BROWN RD, JONES G, WILLETT P, et al., 2002, MATCHING 2-DIMENSIONAL CHEMICAL GRAPHS USING GENETIC ALGORITHMS, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 34, Pages: 63-70, ISSN: 0095-2338
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- Citations: 37
CLARK DE, JONES G, WILLETT P, et al., 2002, PHARMACOPHORIC PATTERN-MATCHING IN PILES OF 3-DIMENSIONAL CHEMICAL STRUCTURES - COMPARISON OF CONFORMATIONAL-SEARCHING ALGORITHMS FOR FLEXIBLE SEARCHING, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 34, Pages: 197-206, ISSN: 0095-2338
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- Citations: 79
Xing L, Glen RC, 2002, Novel methods for the prediction of logP, p<i>K</i><sub>a</sub>, and logD, JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, Vol: 42, Pages: 796-805, ISSN: 0095-2338
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- Citations: 133
Selwood DL, Brummell DG, Glen RC, et al., 2001, Solution-phase parallel synthesis of 5-carboxamido 1-benzyl-3-(3-dimethylaminopropyloxy)-1<i>H</i>-pyrazoles as activators of soluble guanylate cyclase with improved oral bioavailability, BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, Vol: 11, Pages: 1089-1092, ISSN: 0960-894X
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- Citations: 20
Jandu KS, Barrett V, Brockwell M, et al., 2001, Discovery of 4-[3-(<i>trans</i>-3-dimethylaminocyclobutyl)-1<i>H</i>-indol-5-ylmethyl]-(4<i>S</i>)-oxazolidin-2-one (4991W93), a 5HT<sub>1B/1D</sub> receptor partial agonist and a potent inhibitor of electrically induced plasma extravasation, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 44, Pages: 681-693, ISSN: 0022-2623
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- Citations: 40
Selwood DL, Brummell DG, Budworth J, et al., 2001, Synthesis and biological evaluation of novel pyrazoles and indazoles as activators of the nitric oxide receptor, soluble guanylate cyclase, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 44, Pages: 78-93, ISSN: 0022-2623
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- Citations: 93
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