Alexander E Tropsha

UNCCH, Eshelman School of Pharmacy, Pharmacy

• Home
• Expert Overview
• Profile
• Publications
• Grants
• Patents
• Similar Experts
• Journals
• Trends
• Institutional Network
• Coauthor Network
• Research Network

Alexander E Tropsha

• Organizations
  University of North Carolina at Chapel Hill
  
  Eshelman School of Pharmacy
  
  Pharmacy
  
  

Help us refine your profile

This is a list of publications by this researcher, listed chronologically starting with the most recent first. New publications appear in this list weekly. The source of publications and 'cited by' data for this application is Scopus.

  Select All    |   Export

• 1.

  2013

  Liying Zhang; Denis Fourches; Alexander Sedykh; Hao Zhu; Alexander Golbraikh; Sean Ekins; Julie Clark; Michele C. Connelly; Martina Sigal; Dena Hodges; et al.

  Discovery of novel antimalarial compounds enabled by QSAR-based virtual screening

  Journal of Chemical Information and Modeling. 2013;53(2):475-492.
  0

• 2.

  2013

  Xiang-Wei Zhu; Alexander Sedykh; Hao Zhu; Shu-Shen Liu; Alexander Tropsha

  The Use of Pseudo-Equilibrium Constant Affords Improved QSAR Models of Human Plasma Protein Binding

  Pharmaceutical Research. 2013:1-9.
  0

• 3.

  2012

  Todd M. Martin; Paul Harten; Douglas M. Young; Eugene N. Muratov; Alexander Golbraikh; Hao Zhu; Alexander Tropsha

  Does rational selection of training and test sets improve the outcome of QSAR modeling?

  Journal of Chemical Information and Modeling. 2012;52(10):2570-2578.
  0

• 4.

  2012

  Raed Khashan; Weifan Zheng; Alexander Tropsha

  Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

  Proteins: Structure, Function and Bioinformatics. 2012;80(9):2207-2217.
  0

• 5.

  2012

  Rima Hajjo; Vincent Setola; Bryan L. Roth; Alexander Tropsha

  Chemocentric informatics approach to drug discovery: Identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers

  Journal of Medicinal Chemistry. 2012;55(12):5704-5719.
  2

• 6.

  2012

  Ahuva Cern; Alexander Golbraikh; Aleck Sedykh; Alexander Tropsha; Yechezkel Barenholz; Amiram Goldblum

  Quantitative structure - Property relationship modeling of remote liposome loading of drugs

  Journal of Controlled Release. 2012;160(2):147-157.
  2

• 7.

  2012

  Hao Tang; Xiang Simon Wang; Jui-Hua Hsieh; Alexander Tropsha

  Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening?

  Proteins: Structure, Function and Bioinformatics. 2012;80(6):1503-1521.
  4

• 8.

  2012

  Jui-Hua Hsieh; Shuangye Yin; Xiang S. Wang; Shubin Liu; Nikolay V. Dokholyan; Alexander Tropsha

  Cheminformatics meets molecular mechanics: A combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening

  Journal of Chemical Information and Modeling. 2012;52(1):16-28.
  5

• 9.

  2012

  Elizabeth A. Proctor; Shuangye Yin; Alexander Tropsha; Nikolay V. Dokholyan

  Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets

  Biophysical Journal. 2012;102(1):144-151.
  1

• 10.

  2012

  Alexander Sedykh; Denis Fourches; Jianmin Duan; Oliver Hucke; Michel Garneau; Hao Zhu; Pierre Bonneau; Alexander Tropsha

  Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions

  Pharmaceutical Research. 2012:1-12.
  0

• 11.

  2012

  Eric F. Lock; Nour Abdo; Ruili Huang; Menghang Xia; Oksana Kosyk; Shannon H. O'Shea; Yi-Hui Zhou; Alexander Sedykh; Alexander Tropsha; Christopher P. Austin; et al.

  Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model

  Toxicological Sciences. 2012;126(2):578-588.
  4

• 12.

  2012

  Ivan Rusyn; Alexander Sedykh; Yen Low; Kathryn Z. Guyton; Alexander Tropsha

  Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data

  Toxicological Sciences. 2012;127(1):1-9.
  3

• 13.

  2011

  Sarel J. Fleishman; Timothy A. Whitehead; Eva-Maria Strauch; Jacob E. Corn; Sanbo Qin; Huan-Xiang Zhou; Julie C. Mitchell; Omar N.A. Demerdash; Mayuko Takeda-Shitaka; Genki Terashi; et al.

  Community-wide assessment of protein-interface modeling suggests improvements to design methodology

  Journal of Molecular Biology. 2011;414(2):289-302.
  17

• 14.

  2011

  Jui-Hua Hsieh; Shuangye Yin; Shubin Liu; Alexander Sedykh; Nikolay V. Dokholyan; Alexander Tropsha

  Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets

  Journal of Chemical Information and Modeling. 2011;51(9):2027-2035.
  4

• 15.

  2011

  Daniel Samarov; J.S. Marron; Yufeng Liu; Christopher Grulke; Alexander Tropsha

  Local kernel canonical correlation analysis with application to virtual drug screening

  Annals of Applied Statistics. 2011;5(3):2169-2196.
  0

• 16.

  2011

  Yen Low; Takeki Uehara; Yohsuke Minowa; Hiroshi Yamada; Yasuo Ohno; Tetsuro Urushidani; Alexander Sedykh; Eugene Muratov; Viktor Kuzmin; Denis Fourches; et al.

  Predicting drug-induced hepatotoxicity using QSAR and toxicogenomics approaches

  Chemical Research in Toxicology. 2011;24(8):1251-1262.
  16

• 17.

  2011

  Alexander Tropsha; Alexander Golbraikh; Won-Jea Cho

  Development of kNN QSAR models for 3-arylisoquinoline antitumor agents

  Bulletin of the Korean Chemical Society. 2011;32(7):2397-2404.
  0

• 18.

  2011

  Denis Fourches; Dongqiuye Pu; Alexander Tropsha

  Exploring quantitative nanostructure-activity relationships (QNAR) modeling as a tool for predicting biological effects of manufactured nanoparticles

  Combinatorial Chemistry and High Throughput Screening. 2011;14(3):217-225.
  6

• 19.

  2011

  Alexander Sedykh; Hao Zhu; Hao Tang; Liying Zhang; Ann Richard; Ivan Rusyn; Alexander Tropsha

  Use of in Vitro HTS-derived concentration-response data as biological descriptors improves the accuracy of QSAR models of in Vivo Toxicity

  Environmental Health Perspectives. 2011;119(3):364-370.
  10

• 20.

  2011

  Tudor I Oprea; Elebeoba E May; Andrei Leitão; Alexander Tropsha

  Computational systems chemical biology.

  Methods in molecular biology (Clifton, N.J.). 2011;672:459-488.
  5

• 21.

  2011

  Jerry O Ebalunode; Weifan Zheng; Alexander Tropsha

  Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design.

  Methods in molecular biology (Clifton, N.J.). 2011;685:111-133.
  9

• 22.

  2010

  Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Artem Cherkasov; Jiazhong Li; Paola Gramatica; Katja Hansen; Timon Schroeter; Klaus-Robert Müller; et al.

  Applicability domains for classification problems: Benchmarking of distance to models for ames mutagenicity set

  Journal of Chemical Information and Modeling. 2010;50(12):2094-2111.
  22

• 23.

  2010

  Theo Walker; Christopher M. Grulke; Diane Pozefsky; Alexander Tropsha

  Chembench: A cheminformatics workbench

  Bioinformatics. 2010;26(23):3000-3001.
  13

• 24.

  2010

  Rima Hajjo; Christopher M. Grulke; Alexander Golbraikh; Vincent Setola; Xi-Ping Huang; Bryan L. Roth; Alexander Tropsha

  Development, validation, and use of quantitative structure-activity relationship models of 5-hydroxytryptamine (2B) receptor ligands to identify novel receptor binders and putative valvulopathic compounds among common drugs

  Journal of Medicinal Chemistry. 2010;53(21):7573-7586.
  6

• 25.

  2010

  Denis Fourches; Dongqiuye Pu; Carlos Tassa; Ralph Weissleder; Stanley Y. Shaw; Russell J. Mumper; Alexander Tropsha

  Quantitative nanostructure - Activity relationship modeling

  ACS Nano. 2010;4(10):5703-5712.
  29

• 26.

  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. 2010;14(5):1137-1143.
  1

• 27.

  2010

  Denis Fourches; Eugene Muratov; Alexander Tropsha

  Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research

  Journal of Chemical Information and Modeling. 2010;50(7):1189-1204.
  39

• 28.

  2010

  Alexander Tropsha

  Best practices for QSAR model development, validation, and exploitation

  Molecular Informatics. 2010;29(6-7):476-488.
  79

• 29.

  2010

  Amie D. Rodgers; Hao Zhu; Denis Fourches; Ivan Rusyn; Alexander Tropsha

  Modeling liver-related adverse effects of drugs using k nearest neighbor quantitative structure-activity relationship method

  Chemical Research in Toxicology. 2010;23(4):724-732.
  12

• 30.

  2010

  Denis Fourches; Julie C. Barnes; Nicola C. Day; Paul Bradley; Jane Z. Reed; Alexander Tropsha

  Cheminformatics analysis of assertions mined from literature that describe drug-induced liver injury in different species

  Chemical Research in Toxicology. 2010;23(1):171-183.
  23

• 31.

  2009

  Hao Zhu; Todd M. Martin; Lin Ye; Alexander Sedykh; Douglas M. Young; Alexander Tropsha

  Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure

  Chemical Research in Toxicology. 2009;22(12):1913-1921.
  17

• 32.

  2009

  Antony J. Williams; Valery Tkachenko; Chris Lipinski; Alexander Tropsha; Sean Ekins

  Free online resources enabling crowd-sourced drug discovery

  Drug Discovery World. 2009;11(1):33-39.
  11

• 33.

  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: I. Method development

  Journal of Computer-Aided Molecular Design. 2009;23(11):773-784.
  5

• 34.

  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. 2009;23(11):785-797.
  3

• 35.

  2009

  Yuri K. Peterson; Xiang S. Wang; Patrick J. Casey; Alexander Tropsha

  Discovery of geranylgeranyltransferase-I inhibitors with novel scaffolds by the means of quantitative structure-activity relationship modeling, virtual screening, and experimental validation

  Journal of Medicinal Chemistry. 2009;52(14):4210-4220.
  12

• 36.

  2009

  Sean Ekins; Alexander Tropsha

  A turning point for blood-brain barrier modeling

  Pharmaceutical Research. 2009;26(5):1283-1284.
  3

• 37.

  2009

  Hao Tang; Xiang S. Wang; Xi-Ping Huang; Bryan L. Roth; Kyle V. Butler; Alan P. Kozikowski; Mira Jung; Alexander Tropsha

  Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening, and experimental validation

  Journal of Chemical Information and Modeling. 2009;49(2):461-476.
  22

• 38.

  2009

  A. Tropsha; D. Fourches

  Graph representation of molecular datasets: Applications to dataset visualization and comparison using graph indices

  Chemistry Central Journal. 2009;3(SUPPL. 1).
  0

• 39.

  2009

  Hao Zhu; Li Ye; Ann Richard; Alexander Golbraikh; Fred A. Wright; Ivan Rusyn; Alexander Tropsha

  A novel two-step hierarchical quantitative structure-activity relationship modeling work flow for predicting acute toxicity of chemicals in rodents

  Environmental Health Perspectives. 2009;117(8):1257-1264.
  10

• 40.

  2008

  Shuxing Zhang; Andrew H. Kaplan; Alexander Tropsha

  HIV-1 protease function and structure studies with the simplicial neighborhood analysis of protein packing method

  Proteins: Structure, Function and Genetics. 2008;73(3):742-753.
  2

• 41.

  2008

  Igor V. Tetko; Iurii Sushko; Anil Kumar Pandey; Hao Zhu; Alexander Tropsha; Ester Papa; Tomas Öberg; Roberto Todeschini; Denis Fourches; Alexandre Varnek

  Critical assessment of QSAR models of environmental toxicity against tetrahymena pyriformis: Focusing on applicability domain and overfitting by variable selection

  Journal of Chemical Information and Modeling. 2008;48(9):1733-1746.
  89

• 42.

  2008

  Liying Zhang; Hao Zhu; Tudor I. Oprea; Alexander Golbraikh; Alexander Tropsha

  QSAR modeling of the blood-brain barrier permeability for diverse organic compounds

  Pharmaceutical Research. 2008;25(8):1902-1914.
  47

• 43.

  2008

  Xiang S. Wang; Hao Tang; Alexander Golbraikh; Alexander Tropsha

  Combinatorial QSAR modeling of specificity and subtype selectivity of ligands binding to serotonin receptors 5HT1E and 5HT1F

  Journal of Chemical Information and Modeling. 2008;48(5):997-1013.
  12

• 44.

  2008

  M. Karthikeyan; S. Krishnan; Anil Kumar Pandey; Andreas Bender; Alexander Tropsha

  Distributed chemical computing using ChemStar: An open source java remote method invocation architecture applied to large scale molecular data from PubChem

  Journal of Chemical Information and Modeling. 2008;48(4):691-703.
  4

• 45.

  2008

  Hao Zhu; Alexander Tropsha; Denis Fourches; Alexandre Varnek; Ester Papa; Paola Gramatical; Tomas Öberg; Phuong Dao; Artem Cherkasov; Igor V. Tetko

  Combinatorial QSAR modeling of chemical toxicants tested against Tetrahymena pyriformis

  Journal of Chemical Information and Modeling. 2008;48(4):766-784.
  75

• 46.

  2008

  Hao Zhu; Ivan Rusyn; Ann Richard; Alexander Tropsha

  Use of cell viability assay date improves the prediction accuracy of conventional quantitative structure-activity relationships models of animal carcinogenicity

  Environmental Health Perspectives. 2008;116(4):506-513.
  25

• 47.

  2008

  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

  Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. 2008:199-206.
  0

• 48.

  2008

  Jui-Hua Hsieh; Xiang S. Wang; Denise Teotico; Alexander Golbraikh; Alexander Tropsha

  Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening

  Journal of Computer-Aided Molecular Design. 2008;22(9):593-609.
  13

• 49.

  2007

  Alexander Tropsha; Alexander Golbraikh

  Predictive QSAR modeling workflow, model applicability domains, and virtual screening

  Current Pharmaceutical Design. 2007;13(34):3494-3504.
  95

• 50.

  2007

  Tudor I. Oprea; Alexander Tropsha; Jean-Loup Faulon; Mark D. Rintoul

  Systems chemical biology

  Nature Chemical Biology. 2007;3(8):447-450.
  57

• 51.

  2007

  Shuxing Zhang; Linyi Wei; Ken Bastow; Weifan Zheng; Arnold Brossi; Kuo-Hsiung Lee; Alexander Tropsha

  Antitumor agents 252. Application of validated QSAR models to database mining: Discovery of novel tylophorine derivatives as potential anticancer agents

  Journal of Computer-Aided Molecular Design. 2007;21(1-3):97-112.
  44

• 52.

  2006

  Tudor I. Oprea; Alexander Tropsha

  Cheminformatics and drug discovery

  Drug Discovery Today: Technologies. 2006;3(4):355-356.
  0

• 53.

  2006

  Tudor I. Oprea; Alexander Tropsha

  Target, chemical and bioactivity databases - integration is key

  Drug Discovery Today: Technologies. 2006;3(4):357-365.
  18

• 54.

  2006

  Joseph R. Votano; Marc Parham; L. Mark Hall; Lowell H. Hall; Lemont B. Kier; Scott Oloff; Alexander Tropsha

  QSAR modeling of human serum protein binding with several modeling techniques utilizing structure-information representation

  Journal of Medicinal Chemistry. 2006;49(24):7169-7181.
  46

• 55.

  2006

  Ola M. Ghoneim; Jacqueline A. Legere; Alexander Golbraikh; Alexander Tropsha; Raymond G. Booth

  Novel ligands for the human histamine H₁ receptor: Synthesis, pharmacology, and comparative molecular field analysis studies of 2-dimethylamino-5-(6)-phenyl-1,2,3,4-tetrahydronaphthalenes

  Bioorganic and Medicinal Chemistry. 2006;14(19):6640-6658.
  10

• 56.

  2006

  Alan P. Kozikowski; Bryan Roth; Alexander Tropsha

  Why academic drug discovery makes sense [2]

  Science. 2006;313(5791):1235-1236.
  15

• 57.

  2006

  Shuxing Zhang; Alexander Golbraikh; Scott Oloff; Harold Kohn; Alexander Tropsha

  A novel Automated Lazy Learning QSAR (ALL-QSAR) approach: Method development, applications, and virtual screening of chemical databases using validated ALL-QSAR models

  Journal of Chemical Information and Modeling. 2006;46(5):1984-1995.
  58

• 58.

  2006

  Deepak Bandyopadhyay; Jun Huan; Jinze Liu; Jan Prins; Jack Snoeyink; Wei Wang; Alexander Tropsha

  Structure-based function inference using protein family-specific fingerprints

  Protein Science. 2006;15(6):1537-1543.
  22

• 59.

  2006

  Shuxing Zhang; Alexander Golbraikh; Alexander Tropsha

  Development of quantitative structure-binding affinity relationship models based on novel geometrical chemical descriptors of the protein-ligand interfaces

  Journal of Medicinal Chemistry. 2006;49(9):2713-2724.
  36

• 60.

  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. 2006;46(3):1245-1254.
  58

• 61.

  2006

  Scott Oloff; Shuxing Zhang; Nagamani Sukumar; Curt Breneman; Alexander Tropsha

  Chemometric analysis of ligand receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)

  Journal of Chemical Information and Modeling. 2006;46(2):844-851.
  32

• 62.

  2006

  A. Tropsha; S.X. Wang

  QSAR modeling of GPCR ligands: methodologies and examples of applications.

  Ernst Schering Foundation symposium proceedings. 2006;(2):49-73.
  6

• 63.

  2006

  Alexander Tropsha

  Chapter 7 Variable Selection QSAR Modeling, Model Validation, and Virtual Screening

  Annual Reports in Computational Chemistry. 2006;2(C):113-126.
  8

• 64.

  2006

  Xin Chen; Alexander Tropsha

  Calculation of the relative binding affinity of enzyme inhibitors using the generalized linear response method

  Journal of Chemical Theory and Computation. 2006;2(5):1435-1443.
  4

• 65.

  2006

  Jun Huan; Deepak Bandyopadhyay; Jan Prins; Jack Snoeyink; Alexander Tropsha; Wei Wang

  Distance-based identification of structure motifs in proteins using constrained frequent subgraph mining.

  Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 2006:227-238.
  6

• 66.

  2005

  Scott Oloff; Richard B. Mailman; Alexander Tropsha

  Application of validated QSAR models of D₁ dopaminergic antagonists for database mining

  Journal of Medicinal Chemistry. 2005;48(23):7322-7332.
  53

• 67.

  2005

  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. 2005;12(6):657-671.
  24

• 68.

  2005

  Peter Itskowitz; Alexander Tropsha

  K nearest neighbors QSAR modeling as a variational problem: Theory and applications

  Journal of Chemical Information and Modeling. 2005;45(3):777-785.
  23

• 69.

  2005

  Jose Luis Medina-Franco; Alexander Golbraikh; Scott Oloff; Rafael Castillo; Alexander Tropsha

  Quantitative structure-activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining

  Journal of Computer-Aided Molecular Design. 2005;19(4):229-242.
  18

• 70.

  2005

  A. Kovatcheva; A. Golbraikh; S. Oloff; J. Feng; W. Zheng; A. Tropsha

  QSAR modeling of datasets with enantioselective compounds using chirality sensitive molecular descriptors

  SAR and QSAR in Environmental Research. 2005;16(1-2):93-102.
  14

• 71.

  2005

  Alexander Tropsha; Herbert Edelsbrunner

  Biogeometry: applications of computational geometry to molecular structure.

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2005:1-3.
  0

• 72.

  2005

  Alexander Tropsha; Herbert Edelsbrunner

  Biogeometry: Applications of computational geometry to molecular structure

  Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005. 2005:1-3.
  0

• 73.

  2004

  Zhiyan Xiao; Shikha Varma; Yun-De Xiao; Alexander Tropsha

  Modeling of p38 mitogen-activated protein kinase inhibitors using the Catalyst™ HypoGen and k-nearest neighbor QSAR methods

  Journal of Molecular Graphics and Modelling. 2004;23(2):129-138.
  12

• 74.

  2004

  Chee Ng; Yunde Xiao; Wendy Putnam; Bert Lum; Alexander Tropsha

  Quantitative structure-pharmacokinetic parameters relationships (QSPKR) analysis of antimicrobial agents in humans using simulated annealing k-nearest-neighbor and partial least-square analysis methods

  Journal of Pharmaceutical Sciences. 2004;93(10):2535-2544.
  21

• 75.

  2004

  Joseph R. Votano; Marc Parham; Lowell H. Hall; Lemont B. Kier; Scott Oloff; Alexander Tropsha; Qian Xie; Weida Tong

  Three new consensus QSAR models for the prediction of Ames genotoxicity

  Mutagenesis. 2004;19(5):365-377.
  61

• 76.

  2004

  Douglas B. Sherman; Shuxing Zhang; J. Bruce Pitner; Alexander Tropsha

  Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method

  Proteins: Structure, Function and Genetics. 2004;56(4):828-838.
  6

• 77.

  2004

  Suzanne C. Edavettal; Kevin Carrick; Ruchir R. Shah; Lars C. Pedersen; Alexander Tropsha; R. Marshall Pope; Jian Liu

  A Conformational Change in Heparan Sulfate 3-O-Sulfotransferase-1 Is Induced by Binding to Heparan Sulfate

  Biochemistry. 2004;43(16):4680-4688.
  9

• 78.

  2004

  Min Shen; Cécile Béguin; Alexander Golbraikh; James P. Stables; Harold Kohn; Alexander Tropsha

  Application of Predictive QSAR Models to Database Mining: Identification and Experimental Validation of Novel Anticonvulsant Compounds

  Journal of Medicinal Chemistry. 2004;47(9):2356-2364.
  79

• 79.

  2004

  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 Computer Sciences. 2004;44(2):582-595.
  47

• 80.

  2004

  William F. Pendergraft III; Gloria A. Preston; Ruchir R. Shah; Alexander Tropsha; Charles W. Carter Jr.; J. Charles Jennette; Ronald J. Falk

  Autoimmunity is triggered by cPR-3(105-201), a protein complementary to human autoantigen proteinase-3

  Nature Medicine. 2004;10(1):72-79.
  157

• 81.

  2004

  Jun Huan; Wei Wang; Deepak Bandyopadhyay; Jack Snoeyink; Jan Prins; Alexander Tropsha

  Mining protein family specific residue packing patterns from protein structure graphs

  Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB. 2004;8:308-315.
  29

• 82.

  2004

  J. Huan; W. Wang; A. Washington; J. Prins; R. Shah; A. Tropsha

  Accurate classification of protein structural families using coherent subgraph analysis.

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2004:411-422.
  22

• 83.

  2004

  Scott Oloff; Eric Reihl; Alex Tropsha; Chuck Kessler; Terry O'Brien; Mike Blocksome; Madhu Gombar; Virinder Batra; Rich Dulaney

  Novel automated, grid based, web accessible technology for computer-aided drug discovery

  Technology for Life: North Carolina Symposium on Biotechnology and Bioinformatics - 2004 Proceedings. 2004:141-152.
  0

• 84.

  2003

  Bala Krishnamoorthy; Alexander Tropsha

  Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

  Bioinformatics. 2003;19(12):1540-1548.
  64

• 85.

  2003

  Min Shen; Yunde Xiao; Alexander Golbraikh; Vijay K. Gombar; Alexander Tropsha

  Development and validation of κ-nearest-neighbor QSPR models of metabolic stability of drug candidates

  Journal of Medicinal Chemistry. 2003;46(14):3013-3020.
  78

• 86.

  2003

  Alexander Tropsha; Paola Gramatica; Vijay K. Gombar

  The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models

  QSAR and Combinatorial Science. 2003;22(1):69-77.
  601

• 87.

  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. 2003;17(2-4):241-253.
  187

• 88.

  2003

  Alexander Golbraikh; Alexander Tropsha

  QSAR modeling using chirality descriptors derived from molecular topology

  Journal of Chemical Information and Computer Sciences. 2003;43(1):144-154.
  64

• 89.

  2003

  Alexander Tropsha; Charles W. Carter Jr.; Stephen Cammer; Iosif I. Vaisman

  Simplicial Neighborhood Analysis of Protein Packing (SNAPP): A Computational Geometry Approach to Studying Proteins

  Methods in Enzymology. 2003;374:509-544.
  25

• 90.

  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. 2002;42(4):769-787.
  34

• 91.

  2002

  Min Shen; Arnaud LeTiran; Yunde Xiao; Alexander Golbraikh; Harold Kohn; Alexander Tropsha

  Quantitative structure-activity relationship analysis of functionalized amino acid anticonvulsant agents using k nearest neighbor and simulated annealing PLS methods

  Journal of Medicinal Chemistry. 2002;45(13):2811-2823.
  68

• 92.

  2002

  Zhiyan Xiao; Yun-De Xiao; Jun Feng; Alexander Golbraikh; Alexander Tropsha; Kuo-Hsiung Lee

  Antitumor agents. 213. Modeling of epipodophyllotoxin derivatives using variable selection k nearest neighbor QSAR method

  Journal of Medicinal Chemistry. 2002;45(11):2294-2309.
  59

• 93.

  2002

  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. 2002;16(5-6):357-369.
  141

• 94.

  2002

  Alexander Golbraikh; Alexander Tropsha

  Beware of q²!

  Journal of Molecular Graphics and Modelling. 2002;20(4):269-276.
  1162

• 95.

  2002

  Alexander Tropsha; Charles H. Reynolds

  Designing focused libraries for drug discovery: Hit to lead to drug

  Journal of Molecular Graphics and Modelling. 2002;20(6):427-428.
  8

• 96.

  2002

  Alexander Tropsha; Weifan Zheng

  Rational principles of compound selection for combinatorial library design

  Combinatorial Chemistry and High Throughput Screening. 2002;5(2):111-123.
  21

• 97.

  2001

  Charles W. Carter Jr.; Brendan C. Lefebvre; Stephen A. Cammer; Alexander Tropsha; Marshall Hall Edgell

  Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations

  Journal of Molecular Biology. 2001;311(4):625-638.
  77

• 98.

  2001

  Hin Hark Gan; Alexander Tropsha; Tamar Schlick

  Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily

  Proteins: Structure, Function and Genetics. 2001;43(2):134-144.
  89

• 99.

  2001

  Christian Pilger; Cecilia Bartolucci; Doriano Lamba; Alexander Tropsha; Gregor Fels

  Accurate prediction of the bound conformation of galanthamine in the active site of Torpedo californica acetylcholinesterase using molecular docking

  Journal of Molecular Graphics and Modelling. 2001;19(3-4):288-296.
  27

• 100.

  2001

  A. Tropsha; W. Zheng

  Identification of the descriptor pharmacophores using variable selection QSAR: Applications to database mining

  Current Pharmaceutical Design. 2001;7(7):599-612.
  39

• 101.

  2001

  Alexander Golbraikh; Danail Bonchev; Alexander Tropsha

  Novel Chirality Descriptors Derived from Molecular Topology

  Journal of Chemical Information and Computer Sciences. 2001;41(1):147-158.
  82

• 102.

  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. 2001;41(6):1470-1477.
  22

• 103.

  2000

  Hin Hark Gan; Alexander Tropsha; Tamar Schlick

  Generating folded protein structures with a lattice chain growth algorithm

  Journal of Chemical Physics. 2000;113(13):5511-5524.
  12

• 104.

  2000

  Shun-Xiang Zhang; Jun Feng; Sheng-Chu Kuo; Arnold Brossi; Ernest Hamel; Alexander Tropsha; Kuo-Hsiung Lee

  Antitumor agents. 199. Three-dimensional quantitative structure-activity relationship study of the colchicine binding site ligands using comparative molecular field analysis

  Journal of Medicinal Chemistry. 2000;43(2):167-176.
  79

• 105.

  2000

  Xie Dexuan; 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. 2000;40(1):167-177.
  22

• 106.

  2000

  Alexander Tropsha

  Recent trends in computer-aided drug discovery

  Current Opinion in Drug Discovery and Development. 2000;3(3):310-313.
  8

• 107.

  2000

  Alexander Golbraikh; Alexander Tropsha

  Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection

  Molecular Diversity. 2000;5(4):231-243.
  42

• 108.

  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. 2000;40(1):185-194.
  228

• 109.

  1999

  Thomas M. O'Connell; Lu Wang; Alexander Tropsha; Jan Hermans

  The 'random-coil' state of proteins: Comparison of database statistics and molecular simulations

  Proteins: Structure, Function and Genetics. 1999;36(4):407-418.
  23

• 110.

  1999

  Brian Hoffman; Sung Jin Cho; Weifan Zheng; Steven Wyrick; David E. Nichols; Richard B. Mailman; Alexander Tropsha

  Quantitative structure-activity relationship modeling of dopamine D₁ antagonists using comparative molecular field analysis, genetic algorithms- partial least-squares, and K nearest neighbor methods

  Journal of Medicinal Chemistry. 1999;42(17):3217-3226.
  71

• 111.

  1999

  Ehren C. Bucholtz; Randal L. Brown; Alexander Tropsha; Raymond G. Booth; Steven D. Wyrick

  Synthesis, evaluation, and comparative molecular field analysis of 1- phenyl-3-amino-1,2,3,4-tetrahydronaphthalenes as ligands for histamine H₁ receptors

  Journal of Medicinal Chemistry. 1999;42(16):3041-3054.
  28

• 112.

  1999

  Xin Chen; Alexander Tropsha

  Generalized linear response method: Application to hydration free energy calculations

  Journal of Computational Chemistry. 1999;20(8):749-759.
  4

• 113.

  1999

  A. Tropsha; S.J. Cho; W. Zheng

  "New tricks for an old dog": Development and application of novel QSAR methods for rational design of combinatorial chemical libraries and database mining

  ACS Symposium Series. 1999;719:198-211.
  3

• 114.

  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. 1999;39(4):738-746.
  36

• 115.

  1999

  Xin Chen; Andrew Rusinko III; Alexandler Tropsha; S. Stanley Young

  Automated pharmacophore identification for large chemical data sets

  Journal of Chemical Information and Computer Sciences. 1999;39(5):887-896.
  62

• 116.

  1999

  Ehren C. Bucholtz; Alexander Tropsha

  The effect of region size on CoMFA analyses

  Medicinal Chemistry Research. 1999;9(9):675-685.
  5

• 117.

  1998

  Qian Shi; Ke Chen; Xin Chen; Arnold Brossi; Pascal Verdier-Pinard; Ernest Hamel; Andrew T. McPhail; Alexander Tropsha; Kuo-Hsiung Lee

  Antitumor Agents. 183. Syntheses, Conformational Analyses, and Antitubulin Activity of Allothiocolchicinoids

  Journal of Organic Chemistry. 1998;63(12):4018-4025.
  24

• 118.

  1998

  S. Gary Mansfield; Steven Cammer; Steven C. Alexander; David P. Muehleisen; Rosemary S. Gray; Alexander Tropsha; Walter E. Bollenbacher

  Molecular cloning and characterization of an invertebrate cellular retinoic acid binding protein

  Proceedings of the National Academy of Sciences of the United States of America. 1998;95(12):6825-6830.
  31

• 119.

  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. 1998;38(2):259-268.
  49

• 120.

  1998

  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. 1998;38(2):251-258.
  61

• 121.

  1998

  Weifan Zheng; Sung Jin Cho; Alexander Tropsha

  Rational design of a targeted combinatorial chemical library with opiatelike activity

  International Journal of Quantum Chemistry. 1998;69(1):65-75.
  7

• 122.

  1998

  S.J. Cho; W. Zheng; A. Tropsha

  Focus-2D: a new approach to the design of targeted combinatorial chemical libraries.

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1998:305-316.
  3

• 123.

  1998

  Alexander Tropsha; Sung Jin Cho

  Cross-Validated R² Guided Region Selection for CoMFA Studies

  Perspectives in Drug Discovery and Design. 1998;12--14:57-69.
  3

• 124.

  1997

  W. Zheng; S.J. Cho; I.I. Vaisman; A. Tropsha

  A new approach to protein fold recognition based on Delaunay tessellation of protein structure.

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1997:486-497.
  13

• 125.

  1996

  Sung Jin Cho; Maria Luisa Serrano Garsia; Jim Bier; Alexander Tropsha

  Structure-based alignment and comparative molecular field analysis of acetylcholinesterase inhibitors

  Journal of Medicinal Chemistry. 1996;39(26):5064-5071.
  62

• 126.

  1996

  Lu Wang; Thomas O'Connell; Alexander Tropsha; Jan Hermans

  Molecular simulations of β-sheet twisting

  Journal of Molecular Biology. 1996;262(2):283-293.
  33

• 127.

  1996

  Sung Jin Cho; Alexander Tropsha; Matthew Sufness; Yung-Chi Cheng; Kuo-Hsiung Lee

  Antitumor agents. 163. Three-dimensional quantitative structure-activity relationship study of 4′-O-demethylepipodophyllotoxin analogs using the modified CoMFA/q²-GRS approach

  Journal of Medicinal Chemistry. 1996;39(7):1383-1395.
  74

• 128.

  1996

  David M. Mottola; Sergei Laiter; Val J. Watts; Alexander Tropsha; Steven D. Wyrick; David E. Nichols; Richard B. Mailman

  Conformational analysis of D₁ dopamine receptor agonists: Pharmacophore assessment and receptor mapping

  Journal of Medicinal Chemistry. 1996;39(1):285-296.
  45

• 129.

  1996

  Lu Wang; Thomas O'Connell; Alexander Tropsha; Jan Hermans

  Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system

  Biopolymers. 1996;39(4):479-489.
  19

• 130.

  1996

  A. Tropsha; R.K. Singh; I.I. Vaisman; W. Zheng

  Statistical geometry analysis of proteins: implications for inverted structure prediction.

  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1996:614-623.
  14

• 131.

  1995

  Lu Wang; Thomas O'Connell; Alexander Tropsha; Jan Hermans

  Thermodynamic parameters for the helix-coil transition of oligopeptides: Molecular dynamics simulation with the peptide growth method

  Proceedings of the National Academy of Sciences of the United States of America. 1995;92(24):10924-10928.
  21

• 132.

  1995

  Yibing Yan; Bruce W. Erickson; Alexander Tropsha

  Free energies for folding and refolding of four types of β turns: Simulation of the role of D/L chirality

  Journal of the American Chemical Society. 1995;117(29):7592-7599.
  22

• 133.

  1995

  Kalpana Krishnaswami; Alexander Tropsha; Philip C. Smith

  Semi-empirical calculations of intramolecular acyl transfer in cis-enols of O-aroyl acetylacetones

  Journal of Molecular Structure: THEOCHEM. 1995;332(1-2):85-91.
  0

• 134.

  1995

  X. Chen; A. Tropsha

  Relative binding free energies of peptide inhibitors of HIV-1 protease: The influence of the active site protonation state

  Journal of Medicinal Chemistry. 1995;38(1):42-48.
  38

• 135.

  1995

  S. Laiter; D.L. Hoffman; R.K. Singh; I.I. Vaisman; A. Tropsha

  Pseudotorsional OCCO backbone angle as a single descriptor of protein secondary structure

  Protein Science. 1995;4(8):1633-1643.
  9

• 136.

  1995

  D.L. Hoffman; S. Laiter; R.K. Singh; I.I. Vaisman; A. Tropsha

  Rapid protein structure classification using one-dimensional structure profiles on the BioSCAN parallel computer

  Computer Applications in the Biosciences. 1995;11(6):675-679.
  3

• 137.

  1995

  Sung Jin Cho; Alexander Tropsha

  Cross-validated R²-guided region selection for comparative molecular field analysis: A simple method to achieve consistent results

  Journal of Medicinal Chemistry. 1995;38(7):1060-1066.
  217

• 138.

  1994

  Yi-Lin Zhang; Alexander Tropsha; Andrew T. McPhail; Kuo-Hsiung Lee

  Antitumor agents. 152. In vitro inhibitory activity of etoposide derivative NPF against human tumor cell lines and a study of its conformation by X-ray crystallography, molecular modeling, and NMR spectroscopy

  Journal of Medicinal Chemistry. 1994;37(10):1460-1464.
  27

• 139.

  1994

  J.E. Rozzelle Jr.; A. Tropsha; B.W. Erickson

  Rational design of a three-heptad coiled-coil protein and comparison by molecular dynamics simulation with the GCN4 coiled coil: Presence of interior three-center hydrogen bonds

  Protein Science. 1994;3(2):345-355.
  8

• 140.

  1994

  Iosif I. Vaisman; Frank K. Brown; Alexander Tropsha

  Distance dependence of water structure around model solutes

  Journal of Physical Chemistry. 1994;98(21):5559-5564.
  43

• 141.

  1993

  Y. Yan; A. Tropsha; J. Hermans; B.W. Erickson

  Free energies for refolding of the common β turn into the inverse-common β turn: Simulation of the role of D/L chirality

  Proceedings of the National Academy of Sciences of the United States of America. 1993;90(16):7898-7902.
  17

• 142.

  1992

  A. Tropsha; J.S. Kizer; I.M. Chaiken

  Making sense from antisense: a review of experimental data and developing ideas on sense--antisense peptide recognition.

  Journal of molecular recognition : JMR. 1992;5(2):43-54.
  29

• 143.

  1992

  A. Tropsha; J. Hermans

  Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HIV protease

  Protein Engineering. 1992;5(1):29-33.
  26

• 144.

  1991

  John S. Kizer; Alexander Tropsha

  A motif found in propeptides and prohormones that may target them to secretory vesicles

  Biochemical and Biophysical Research Communications. 1991;174(2):586-592.
  24

• 145.

  1991

  Alexander Tropsha; J. Phillip Bowen; Frank K. Brown; J.S. Kizer

  Do interhelical side chain-backbone hydrogen bonds participate in formation of leucine zipper coiled coils?

  Proceedings of the National Academy of Sciences of the United States of America. 1991;88(21):9488-9492.
  7

• 146.

  1985

  A.E. Tropsha; S.V. Nizhnii; L.S. Iaguzhinskii

  Structure-activity relationship in the series of muscarinic acetylcholine receptor agonists: three types of agonist-receptor complexes

  Bioorganicheskaia khimiia. 1985;11(10):1391-1401.
  0

• 147.

  1985

  A.E. Tropsha; S.V. Nizhnii; L.S. Iaguzhinskii

  Structure-activity relationship in the series of muscarinic acetylcholine receptor antagonists: four types of antagonist-receptor binding

  Bioorganicheskaia khimiia. 1985;11(10):1402-1416.
  2

• 148.

  1984

  A.E. Tropsha; A.B. Rakhmaninova; L.S. Iaguzhinskii

  Configuration and properties of a binding site for thyroid hormones on a specific receptor

  Bioorganicheskaia khimiia. 1984;10(4):483-492.
  4

• 149.

  1984

  M.V. Tsybulskaya; N. Antonenko Yu.; A.E. Tropsha; L.S. Yaguzhinsky

  Iodine-containing hormones are dipole modifiers of the phospholipid membranes

  Biofizika. 1984;29(5):801-805.
  3

• 150.

  1984

  M.V. Tsybul'skaya; Yu.N. Antonenko; A.E. Tropsha; L.S. Yaguzhinskii

  Iodine-containing hormones-Dipole modifiers of phospholipid membranes

  Biophysics. 1984;29(5):875-880.
  0