Dimitris K. Agrafiotis - researchr alias

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2022

2019

2018

Chemistry, information and Frank: a tribute to Frank BrownDimitris K. Agrafiotis, M. Katharine Holloway, Scott A. Johnson, Charles H. Reynolds, Terry R. Stouch, Alexander Tropsha, Chris L. Waller. jcamd, 32(7):723-729, 2018. [doi]

2013

Stochastic Proximity Embedding: A Simple, Fast and Scalable Algorithm for Solving the Distance Geometry ProblemDimitris K. Agrafiotis, Deepak Bandyopadhyay, Eric Yang. In Antonio Mucherino, Carlile Lavor, Leo Liberti, Nelson Maculan, editors, Distance Geometry: Theory, Methods, and Applications. pages 291-311, Springer, 2013. [doi]

2012

2011

Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical CartridgeDimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev, Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger, Simson Alex, Michael Farnum. jcisd, 51(12):3113-3130, 2011. [doi]

Single R-Group Polymorphisms (SRPs) and R-Cliffs: An Intuitive Framework for Analyzing and Visualizing Activity Cliffs in a Single Analog SeriesDimitris K. Agrafiotis, John J. M. Wiener, Andrew Skalkin, Jeremy Kolpak. jcisd, 51(5):1122-1131, 2011. [doi]

Library Enhancement through the Wisdom of CrowdsMichael D. Hack, Dmitrii N. Rassokhin, Christophe Buyck, Mark Seierstad, Andrew Skalkin, Peter ten Holte, Todd K. Jones, Taraneh Mirzadegan, Dimitris K. Agrafiotis. jcisd, 51(12):3275-3286, 2011. [doi]

Accelerating Chemical Database Searching Using Graphics Processing UnitsPu Liu, Dimitris K. Agrafiotis, Dmitrii N. Rassokhin, Eric Yang. jcisd, 51(8):1807-1816, 2011. [doi]

Rapid communication reply to comment on: Fast determination of the optimal rotational matrix for macromolecular superpositions Pu Liu, Dimitris K. Agrafiotis, Douglas L. Theobald. jcc, 32(1):185-186, 2011. [doi]

Power Keys: A Novel Class of Topological Descriptors Based on Exhaustive Subgraph Enumeration and their Application in Substructure SearchingPu Liu, Dimitris K. Agrafiotis, Dmitrii N. Rassokhin. jcisd, 51(11):2843-2851, 2011. [doi]

Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New ScaleEric Yang, Pu Liu, Dmitrii N. Rassokhin, Dimitris K. Agrafiotis. jcisd, 51(11):2852-2859, 2011. [doi]

2010

Fast determination of the optimal rotational matrix for macromolecular superpositionsPu Liu, Dimitris K. Agrafiotis, Douglas L. Theobald. jcc, 31(7):1561-1563, 2010. [doi]

2009

2008

A self-organizing algorithm for molecular alignment and pharmacophore developmentDeepak Bandyopadhyay, Dimitris K. Agrafiotis. jcc, 29(6):965-982, 2008. [doi]

2007

Radial Clustergrams: Visualizing the Aggregate Properties of Hierarchical ClustersDimitris K. Agrafiotis, Deepak Bandyopadhyay, Michael Farnum. jcisd, 47(1):69-75, 2007. [doi]

Conformational Sampling of Bioactive Molecules: A Comparative StudyDimitris K. Agrafiotis, Alan C. Gibbs, Fangqiang Zhu, Sergei Izrailev, Eric J. Martin. jcisd, 47(3):1067-1086, 2007. [doi]

Self-organizing superimposition algorithm for conformational samplingFangqiang Zhu, Dimitris K. Agrafiotis. jcc, 28(7):1234-1239, 2007. [doi]

Recursive Distance Partitioning Algorithm for Common Pharmacophore IdentificationFangqiang Zhu, Dimitris K. Agrafiotis. jcisd, 47(4):1619-1625, 2007. [doi]

2006

A Cluster-Based Strategy for Assessing the Overlap between Large Chemical Libraries and Its Application to a Recent AcquisitionMichael F. M. Engels, Alan C. Gibbs, Edward P. Jaeger, Danny Verbinnen, Victor S. Lobanov, Dimitris K. Agrafiotis. jcisd, 46(6):2651-2660, 2006. [doi]

A distance geometry heuristic for expanding the range of geometries sampled during conformational searchSergei Izrailev, Fangqiang Zhu, Dimitris K. Agrafiotis. jcc, 27(16):1962-1969, 2006. [doi]

2005

A Comparison of Particle Swarms Techniques for the Development of Quantitative Structure-Activity Relationship Models for Drug DesignWalter Cedeño, Dimitris K. Agrafiotis. csb 2005: 322-331 [doi]

2003

Stochastic proximity embeddingDimitris K. Agrafiotis. jcc, 24(10):1215-1221, 2003. [doi]

A Geodesic Framework for Analyzing Molecular SimilaritiesDimitris K. Agrafiotis, Huafeng Xu. jcisd, 43(2):475-484, 2003. [doi]

Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regressionWalter Cedeño, Dimitris K. Agrafiotis. jcamd, 17(2-4):255-263, 2003.

Conformational Sampling by Self-OrganizationHuafeng Xu, Sergei Izrailev, Dimitris K. Agrafiotis. jcisd, 43(4):1186-1191, 2003. [doi]

Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple HeuristicHuafeng Xu, Dimitris K. Agrafiotis. jcisd, 43(6):1933-1941, 2003. [doi]

2002

A Fractal Approach for Selecting an Appropriate Bin Size for Cell-Based Diversity EstimationDimitris K. Agrafiotis, Dmitrii N. Rassokhin. jcisd, 42(1):116-122, 2002. [doi]

On the Use of Neural Network Ensembles in QSAR and QSPRDimitris K. Agrafiotis, Walter Cedeño, Victor S. Lobanov. jcisd, 42(4):903-911, 2002. [doi]

Multiobjective optimization of combinatorial librariesDimitris K. Agrafiotis. jcamd, 16(5-6):335-356, 2002. [doi]

A self-organizing principle for learning nonlinear manifoldsDimitris K. Agrafiotis, Huafeng Xu. pnas, 99(25):15869-15872, 2002. [doi]

2001

Multiobjective optimization of combinatorial librariesDimitris K. Agrafiotis. ibmrd, 45(3):545, 2001. [doi]

A Constant Time Algorithm for Estimating the Diversity of Large Chemical LibrariesDimitris K. Agrafiotis. jcisd, 41(1):159-167, 2001. [doi]

Multidimensional scaling and visualization of large molecular similarity tablesDimitris K. Agrafiotis, Dmitrii N. Rassokhin, Victor S. Lobanov. jcc, 22(5):488-500, 2001. [doi]

Multidimensional scaling of combinatorial libraries without explicit enumerationDimitris K. Agrafiotis, Victor S. Lobanov. jcc, 22(14):1712-1722, 2001. [doi]

Design and Prioritization of Plates for High-Throughput ScreeningDimitris K. Agrafiotis, Dmitrii N. Rassokhin. jcisd, 41(3):798-805, 2001. [doi]

A Novel Method for Building Regression Tree Models for QSAR Based on Artificial Ant Colony SystemsSergei Izrailev, Dimitris K. Agrafiotis. jcisd, 41(1):176-180, 2001. [doi]

2000

Nonlinear Mapping NetworksDimitris K. Agrafiotis, Victor S. Lobanov. jcisd, 40(6):1356-1362, 2000. [doi]

Ultrafast Algorithm for Designing Focused Combinational ArraysDimitris K. Agrafiotis, Victor S. Lobanov. jcisd, 40(4):1030-1038, 2000. [doi]

Stochastic Similarity Selections from Large Combinatorial LibrariesVictor S. Lobanov, Dimitris K. Agrafiotis. jcisd, 40(2):460-470, 2000. [doi]

1999

An Efficient Implementation of Distance-Based Diversity Measures Based on k-d TreesDimitris K. Agrafiotis, Victor S. Lobanov. jcisd, 39(1):51-58, 1999. [doi]

1997

On the Use of Information Theory for Assessing Molecular DiversityDimitris K. Agrafiotis. jcisd, 37(3):576-580, 1997. [doi]

Stochastic Algorithms for Maximizing Molecular DiversityDimitris K. Agrafiotis. jcisd, 37(5):841-851, 1997. [doi]

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