Alexander Tropsha

Theo Walker, Christopher M. Grulke, Diane Pozefsky, Alexander Tropsha: Chembench: a cheminformatics workbench. Bioinformatics 26(23): 3000-3001 (2010)

Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha: Functional neighbors: inferring relationships between nonhomologous protein families using family-specific packing motifs. IEEE Transactions on Information Technology in Biomedicine 14(5): 1137-1143 (2010)

Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha: Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development. Journal of Computer-Aided Molecular Design 23(11): 773-784 (2009)

Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha: Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications. Journal of Computer-Aided Molecular Design 23(11): 785-797 (2009)

Alexander Tropsha: QSARModeling. Encyclopedia of Complexity and Systems Science 2009: 7071-7088

Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha: Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs. BIBM 2008: 199-206

Scott Oloff, Shuxing Zhang, Nagamani Sukumar, Curt M. Breneman, Alexander Tropsha: Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). Journal of Chemical Information and Modeling 46(2): 844-851 (2006)

Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha: Combinatorial QSAR Modeling of P-Glycoprotein Substrates. Journal of Chemical Information and Modeling 46(3): 1245-1254 (2006)

Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan Prins, Alexander Tropsha: Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs. Journal of Computational Biology 12(6): 657-671 (2005)

Peter Itskowitz, Alexander Tropsha: k Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications. Journal of Chemical Information and Modeling 45(3): 777-785 (2005)

Alexander Tropsha, Herbert Edelsbrunner: Session Introduction: Biogeometry: Applications of Computational Geometry to Molecular Structure. Pacific Symposium on Biocomputing 2005: 3-4

Assia Kovatcheva, Alexander Golbraikh, Scott Oloff, Yun-De Xiao, Weifan Zheng, Peter Wolschann, Gerhard Buchbauer, Alexander Tropsha: Combinatorial QSAR of Ambergris Fragrance Compounds. Journal of Chemical Information and Modeling 44(2): 582-595 (2004)

Jun Huan, Wei Wang, Anglina Washington, Jan Prins, Ruchir Shah, Alexander Tropsha: Accurate Classification of Protein Structural Families Using Coherent Subgraph Analysis. Pacific Symposium on Biocomputing 2004: 411-422

Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alexander Tropsha: Mining protein family specific residue packing patterns from protein structure graphs. RECOMB 2004: 308-315

Bala Krishnamoorthy, Alexander Tropsha: Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 19(12): 1540-1548 (2003)

Alexander Golbraikh, Min Shen, Zhiyan Xiao, Yun-De Xiao, Kuo-Hsiung Lee, Alexander Tropsha: Rational selection of training and test sets for the development of validated QSAR models. Journal of Computer-Aided Molecular Design 17(2-4): 241-253 (2003)

Alexander Golbraikh, Alexander Tropsha: QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology. Journal of Chemical Information and Computer Sciences 43(1): 144-154 (2003)

Alexander Golbraikh, Alexander Tropsha: Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. Journal of Computer-Aided Molecular Design 16(5-6): 357-369 (2002)

Alexander Golbraikh, Danail Bonchev, Alexander Tropsha: Novel ZE-Isomerism Descriptors Derived from Molecular Topology and Their Application to QSAR Analysis. Journal of Chemical Information and Computer Sciences 42(4): 769-787 (2002)

Alexander Golbraikh, Danail Bonchev, Alexander Tropsha: Novel Chirality Descriptors Derived from Molecular Topology. Journal of Chemical Information and Computer Sciences 41(1): 147-158 (2001)

Charles H. Reynolds, Alexander Tropsha, Lori B. Pfahler, Ross Druker, Subhas Chakravorty, G. Ethiraj, Weifan Zheng: Diversity and Coverage of Structural Sublibraries Selected Using the SAGE and SCA Algorithms. Journal of Chemical Information and Computer Sciences 41(6): 1470-1477 (2001)

Dexuan Xie, Alexander Tropsha, Tamar Schlick: An Efficient Projection Protocol for Chemical Databases: Singular Value Decomposition Combined with Truncated-Newton Minimization. Journal of Chemical Information and Computer Sciences 40(1): 167-177 (2000)

Weifan Zheng, Alexander Tropsha: Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle. Journal of Chemical Information and Computer Sciences 40(1): 185-194 (2000)

Xin Chen, Alexander Tropsha: Generalized linear response method: Application to hydration free energy calculations. Journal of Computational Chemistry 20(8): 749-759 (1999)

Weifan Zheng, Sung Jin Cho, Chris L. Waller, Alexander Tropsha: Rational Combinatorial Library Design. 3. Simulated Annealing Guided Evaluation (SAGE) of Molecular Diversity: A Novel Computational Tool for Universal Library Design and Database Mining. Journal of Chemical Information and Computer Sciences 39(4): 738-746 (1999)

Xin Chen, Andrew Rusinko III, Alexander Tropsha, S. Stanley Young: Automated Pharmacophore Identification for Large Chemical Data Sets1. Journal of Chemical Information and Computer Sciences 39(5): 887-896 (1999)

Weifan Zheng, Sung Jin Cho, Alexander Tropsha: Rational Combinatorial Library Design. 1. Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries. Journal of Chemical Information and Computer Sciences 38(2): 251-258 (1998)

Sung Jin Cho, Weifan Zheng, Alexander Tropsha: Rational Combinatorial Library Design. 2. Rational Design of Targeted Combinatorial Peptide Libraries Using Chemical Similarity Probe and the Inverse QSAR Approaches. Journal of Chemical Information and Computer Sciences 38(2): 259-268 (1998)

Raj K. Singh, Alexander Tropsha, Iosif I. Vaisman: Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues. Journal of Computational Biology 3(2): 213-221 (1996)

D. L. Hoffman, S. Laiter, Raj K. Singh, Iosif I. Vaisman, Alexander Tropsha: Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer. Computer Applications in the Biosciences 11(6): 675-679 (1995)

Xiannong Chen, Libero Bartolotti, Khalid Ishaq, Alexander Tropsha: Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations. Journal of Computational Chemistry 15(3): 333-345 (1994)