2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1995 1994



1. Dimitrov I., Flower D. R., Doytchinova I. AllerTOP – a server for in silico prediction of allergens. BMC Bioinformatic, in press.

2. Patronov, A., Salamanova, E., Dimitrov, I., Flower, D. R., Doytchinova, I. Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations. Curr. Comp.-Aid. Drug Des., in press.




1. Zhivkova, Z., Doytchinova, I. Prediction of steady-state volume of distribution of acidic drugs by quantitative structure – pharmacokinetics relationships. J. Pharm. Sci., 101(3), 1253-1266, 2012 [pdf].

2. Valkova I., Zlatkov A., Krystyna Nedza K., Doytchinova I. Synthesis, 5-HT1A and 5-HT2A receptor affinity and QSAR study of 1-benzhydryl-piperazine derivatives with xanthine moiety at N4. Med. Chem. Res., 21(4), 477-486, 2012 [pdf].

3. Zhivkova, Z., Doytchinova, I. Quantitative structure – plasma protein binding relationships of acidic drugs. J. Pharm. Sci., 101(12), 4627-4641, 2012 [pdf].

4. Patronov, A., Dimitrov, I.Flower, D. R., Doytchinova, I. Peptide binding to HLA-DP2 proteins at pH 5.0 and pH 7.0: a quantitative molecular docking study. BMC Struct. Biol., 12, 20, 2012 [pdf].

5. Yoncheva, K. Doytchinova, I., Tankova, L. Preparation and evaluation of isosorbide mononitrate hydrogels for topical fissure treatment. Curr. Drug Delivery, 9, 452-458, 2012.




1. Bakalova A., Varbanov H., Buyukliev R., Momekov G., Ivanov D., Doytchinova I. Platinum complexes with 5-methyl-5(4-pyridyl)hydantoin and its 3-methyl derivatives: Synthesis and cytotoxic activity – quantitative structure – activity relationships. Arch. Pharm. Chem. Life Sci., 344(4), 209-216, 2011 [pdf].

2. Atanasova, M., Dimitrov, I., Flower, D. R., Doytchinova, I. MHC class II binding prediction by molecular docking. Mol. Informatics, 30(4), 368-375, 2011 [pdf].

3. Dimitrov I., Flower D. R., Doytchinova I. Improving in silico prediction of epitope vaccine candidates by union and intersection of single predictors. World J. Vaccines, 1(2), 15-22, 2011 [pdf].

4. Patronov, A., Dimitrov, I., Flower, D. R., Doytchinova, I. Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct. Biol., 11:32, 2011 [pdf].

5. Doytchinova, I., Petkov, P., Dimitrov, I., Atanasova, M., Flower, D. R. HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci., 20(11), 1918-1928, 2011 [pdf].





1. Dimitrov, I. , P. Garnev, D. R. Flower, I. Doytchinova: Peptide binding to the HLA-DRB1 sypertype: A proteochemometric analysis, Eur. J. Med. Chem., 45(1), 236-243, 2010 [pdf].

2. Solankee, A., K. Kapadia, A. Ćirić, M. Soković, I. Doytchinova, A. Geronikaki: Synthesis of some new S-triazine based chalcones and their derivatives as potent antimicrobial agents, Eur. J. Med. Chem., 45(2), 510-518, 2010 [pdf].

3. Yoncheva, K.,I. Doytchinova, J. M. Irache: Different approaches for determination of the attachment degree of polyethylene glycols to poly(anhydride) nanoparticles, Drug Develop. Ind. Pharm., 36(6), 676-680, 2010 [pdf]

4. Dimitrov, I., P. Garnev, D. R. Flower, I. Doytchinova: MHC clas binding prediction - a little help from a friend. J. Biomed. Biotech., 2010, article ID 705821, 2010 [pdf].

5. Dimitrov, I., P. Garnev, D. R. Flower, I. Doytchinova: EpiTOP - a proteochemometric tool for MHC class II binding prediction. Bioinformatics, 26(16), 2066-2068, 2010 [pdf].

6. D.R. Flower, I.K. Macdonald, K. Ramakrishnan, M.N. Davies, I.A. Doytchinova: Computer-aided selection of candidate vaccine antigens. Immunome Res., 6(Suppl. 2), S1, 2010 [pdf]




1. Tankova, L., K. Yoncheva, D. Kovatchki, I. Doytchinova: Topical and fissure treatment: placebo-controlled study of mononitrate and trinitrate therapies.  Int J. Colorectal Dis., 24(1), 461-464, 2009.

2. Walshe, V. A., Hattotuwagama, C. K., Doytchinova, I., Wong, M., Macdonald, I. K., Mulder, A., Claas, F. H. J., Pellegrino, P., Turner, J., Williams, I., Turnbull, E. L., Borrow, P., Flower, D. R. Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102: A bioinformatic approach to the prediction of new epitopes. PLoS ONE, 4(11), e8095, 2009. [pdf]




1. Doytchinova, I.A., D.R. Flower: Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines.  The Open Vaccine Journal, 1(1), 22-26, 2008. [pdf]

2. Doytchinova, I.A., D.R. Flower: QSAR and the prediction of T-cell epitopes. Current Proteomics, 5(2), 73-95, 2008. [pdf]




1. Doytchinova, I.A., D.R. Flower: Predicting T cell epitopes using multivariate statistics: Comparison of discriminant analysis and multiple linear regression. J. Chem. Inf. Model., 47(1), 234-238, 2007. [pdf]

2. Davies, M. N., P. Guan, M.J. Blythe, J. Salomon, C.P. Toselan, C. Hattotuwagama, V. Walshe, I.A. Doytchinova, D.R. Flower: Using databases and data mining in vaccinology. Expert Opin. Drug Discov., 2(1), 19-35, 2007. [pdf]

3. Hattotuwagama, C.K., P. Guan, M. Davies, D.J. Taylor, V. Walshe, S.L. Hemsley, C. Toseland, I.A. Doytchinova, P. Borrow, D.R. Flower: Empirical, AI, and QSAR Approaches to Peptide – MHC Binding Prediction. In: In silico Immunology. (Eds. D.R. Flower, J. Timmis), Springer, New York, 139-176, 2007.

4. Guan, P., I.A. Doytchinova, D.R. Flower: Identifying Major Histocompatibility Complex Supertypes. In: In silico Immunology. (Eds. D.R. Flower, J. Timmis), Springer, New York, 197-234, 2007.

5. Guan, P., I.A. Doytchinova, D.R. Flower: The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods. In: Immunoinformatics: Predicting Immunogenicity In Silico, Series: Methods in Molecular Biology, Vol. 409, (Ed. D.R. Flower), 143-154, 2007.

6. Hattotuwagama, C., I.A. Doytchinova, D.R. Flower: Towards the Prediction of Class I and II Mouse Major Histocompatibility Complex Peptide Binding Affinity: In Silico Bioinformatic Step by Step Guide Using Quantitative Structure-Activity Relationships. In: Immunoinformatics: Predicting Immunogenicity In Silico, Series: Methods in Molecular Biology, Vol. 409, (Ed. D.R. Flower), 227-245, 2007.

7. Hattotuwagama, C.K., P. Guan, I.A. Doytchinova, D.R. Flower: In Silico QSAR-Based Predictions of Class I and Class II MHC Epitopes. In: Immunoinformatics (Eds. C. Schoenbach, S. Ranganathan, V. Brusic), Sprinder Science+Business Media, LLC, New York , 63 – 89, 2007.

8. Doytchinova, I.A., D.R. Flower: Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine, 25(5), 856-866, 2007. [pdf]

9. Doytchinova, I.A., D.R. Flower: VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines.  BMC Bioinformatics, 8, 4, http://www.biomedcentral.com/1471-2105/8/4, 2007.

10. Slavov, S., M. Atanasova, B. Galabov: QSAR analysis of the anticancer activity of 2,5-disubstituted 9-aza-anthrapyrazoles, QSAR & Comb. Chem., 26(2), 173-181, 2007.

11. Atanasova, M., Ilieva, S., Galabov, B.: QSAR analysis of 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridines with anticancer activity, Eur. J. Med. Chem., 42(9), 1184-1192, 2007.




1.  Vicini, P., M. Incerti, I. A. Doytchinova, P. La Colla, B. Busonera, R. Loddo. Synthesis and antiproliferative activity of benzo[d]isothiazole hydrazones. Eur. J. Med. Chem., 2006, 41, 624-632. [pdf]

2.  Hattotuwagama, C.K., C.P. Toseland, P. Guan, D.J. Taylor, S.L. Hemsley, I.A. Doytchinova, D.R. Flower: Toward Prediction of Class II Mouse Major Histocompatibility Complex Peptide Binding Affinity: In Silico bioinformatic Evaluation Using Partial Least Squares, a Robust Multivariate Statistical Technique. J. Chem. Inf. Model., 46(3), 1491-1502, 2006. [pdf]

3.  Guan, P., I. Doytchinova, C. Hattotuwagama, D.R. Flower: MHCPred 2.0, an updated quantitative T cell epitope prediction server. Appl. Bioinformatics, 5(1), 55-61, 2006. [pdf]

4.  Doytchinova, I.A., D.R. Flower: Class I T cell epitope prediction: improvements using a combination of Proteasome cleavage, TAP affinity, and MHC binding. Mol. Immun., 43(13), 2037-2044, 2006. [pdf]

5.  Doytchinova, I.A., P. Guan, D.R. Flower: EpiJen: a server for multi-step T cell epitope prediction. BMC Bioinformatics, 7, 131, http://www.biomedcentral.com/ 1471-2105/7/131, 2006.

6.  Doytchinova, I.A., D.R. Flower: Modeling the peptide – T cell receptor interaction by the Comparative Molecular Similarity Indices Analysis – Soft Independent Modeling of Class Analogy technique. J. Med. Chem., 49(7), 2193-2199, 2006. [pdf]




1. Doytchinova, I.A., D.R. Flower: In silico identification of supertypes for Class II Major Histocompatibility Complexes. J. Immunol., 174(11), 7085-7095, 2005. [pdf]

2. Doytchinova, I.A., V. Walshe, P. Borrow, D.R. Flower: Towards the chemometric dissection of peptide-HLA-A*0201 binding affinity: comparison of local and global QSAR models. J. Comput. Aid. Mol. Des., 19(3), 203-212, 2005. [pdf]

3. Hattotuwagama, C.K., I.A. Doytchinova, D.R. Flower: In Silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: A Comparative Molecular Similarity Index Analysis (CoMSIA) study. J. Chem. Inf. Model., 45(5), 1415-1426, 2005. [pdf]

4. Guan, P., I.A. Doytchinova, V.A. Walshe, P. Borrow, D.R. Flower: Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for HLA-A*0201. J. Med. Chem., 48(23), 7418-7425, 2005. [pdf]

5. Toseland C.P., D.J. Taylor, H. McSparron, S.L. Hemsley, M.J. Blythe, K. Paine, I.A. Doytchinova, P. Guan, C.K. Hattotuwagama, D.R. Flower: AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical and cellular data. Immunome Res., 1: 4. http://www.immunone-research.com/content/ 1/1/4, 2005. [pdf]

6. Guan, P., M. Davies, D.J. Taylor , S. Wan, H. McSparron, S.L. Hemsley, C. Toseland, M.J. Blythe, P.D. Taylor, V. Walshe, C.K. Hattotuwagama, I.A. Doytchinova, P.V. Coveney, P. Borrow, D.R..Flower: Computational Chemistry, Informatics, and the Discovery of Vaccines. Current Computer-Aided Drug Design, 1(4), 377-398, 2005.




1. Doytchinova, I.A., P. Guan, D. R. Flower. Identifiying human MHC supertypes using bioinformatic methods. J. Immunol., 172(7), 4314 4323, 2004. [pdf]

2. Hattotuwagama, C.K., P. Guan, I.A. Doytchinova, C. Zygouri, D.R. Flower: Quantitative online prediction of peptide binding to the major histocompatibility complex. J. Mol. Graph. Model., 22(3), 195-207, 2004. [pdf]

3. Doytchinova, I.A., V.A. Walshe, N.A. Jones, S.E. Gloster, P. Borrow, D.R. Flower: Coupling in silico and in vitro analysis of peptide–MHC binding: A bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes. J. Immunol., 172(12), 7495-7502, 2004. [pdf]

4. Doytchinova, I.A., S. Hemsley, D.R. Flower: Transporter associated with antigen processing preselection of peptides binding to the MHC: A Bioinformatic evaluation. J. Immunol., 173(11), 6813-6819, 2004. [pdf]

5. Hattotuwagama, C.K., P. Guan, I.A. Doytchinova, D.R. Flower: New horizons in mouse immunoinformatics: 
reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity. Org. Biomol. 
Chem., 2(22), 3274-3283, 2004. [pdf] 

6.Doytchinova, I.A., P. Guan, D.R. Flower: Quantitative structure – activity relationships and the prediction of MHC supermotifs. Methods, 34(4), 444-453, 2004. [pdf]

7. Valkova, I., Vračko, M., Basak, S.C., Modeling of structure-mutagenicity relationships: Counter propagation neural network approach using calculated structural descriptors  Analytica Chimica Acta 509 (2), 179-186, 2004




1. Panico A.M., A. Geronikaki, R. Mgonzo, V. Cardile, B. Gentile, I. Doytchinova. Aminothiazole derivatives with antidegenerative activity on cartilage. Bioorg. & Med. Chem., 11, 2003, 13, 2983 – 2989.

2. Guan P., I.A. Doytchinova, D.R. Flower: HLA-A3-supermotif defined by quantitative structure-activity relationship analysis. Protein Eng., 16(1), 11-18, 2003. [pdf]

3. Guan, P., I.A. Doytchinova, C.Zygouri, D.R. Flower: MHCPred: bringing a  quantitative dimension to the online prediction of MHC binding. Appl. Bioinformatics, 2(1), 63-66, 2003. [pdf]

4. Guan, P., I.A. Doytchinova, C.Zygouri, D.R. Flower: MHCPred: a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res., 31(13), 3621-3624, 2003. [pdf]

5. Guan, P., I.A. Doytchinova, D.R. Flower: A Comparative Molecular Similarity Indices (CoMSIA) study of peptides binding to the HLA-A3 superfamily. Bioorgan. Med. Chem., 11(10), 2307-2311, 2003. [pdf]

6. Doytchinova, I.A., D.R. Flower: The HLA-A2-supermotif: A QSAR definition. Org. Biomol. Chem., 1(15), 2648-2654, 2003. [pdf]

7. McSparron, H., M.J. Blythe, C. Zygouri, I.A. Doytchinova, D.R. Flower: JenPep: A Novel Computational Information Resource for Immunobiology and Vaccinology. J. Chem. Inf. Comp. Sci., 43(4), 1276 – 1287, 2003. [pdf]

8. Doytchinova, I.A., D.R. Flower: Towards the in silico identification of class II restricted T cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction. Bioinformatics, 19(17), 2263 – 2270, 2003. [pdf]

9. Doytchinova, I.A., P. Taylor, D.R. Flower: Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone. J. Biomed. Biotechnol., 2003(5), 267 – 290, 2003. [pdf]

10. Flower, D.R., H. McSparron, M.J. Blythe, C. Zygouri, D. Taylor, P. Guan, S. Wan, P. Coveney, V. Walshe, P. Borrow, I.A. Doytchinova: Computational vaccinology: quantitative approaches. In: Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function, (Eds. G. Bock, J. Goode), Wiley J. & Sons Ltd., Chichester, 102-120, 2003.




1. Doytchinova, I., I. Valkova, R. Natcheva. Adenosine A2A receptor agonists: CoMFA – based selection of the most predictive conformation. SAR QSAR Environ. Res., 13, 2002, 2, 227-235.

2. Vicini P., F. Zani, P. Cozzini, I. Doytchinova. Hydrazones of 1,2-benzisothiazole hydrazides: synthesis, antimicrobial activity and QSAR investigations. Eur. J. Med. Chem., 37, 2002, 553-564.

3. Blythe, M.J., I.A. Doytchinova, D.R. Flower: JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics, 18(3), 434-439, 2002. [pdf]

4. Doytchinova, I.A., M.J. Blythe, D.R. Flower: Additive Method for the Prediction of Protein-Peptide Binding Affinity. Application to the MHC Class I Molecule HLA-A*0201. J. Proteome Res., 1(3), 263-272, 2002. [pdf]

5. Doytchinova, I.A., D.R. Flower: Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: A three-dimensional quantitative structure-activity relationship study. PROTEINS, 48(3), 505-518, 2002. [pdf]

6. Doytchinova, I.A., D.R. Flower: A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J. Comput. Aid. Mol. Des., 16(8-9), 535-544, 2002. [pdf]

7. Doytchinova I.A., D.R. Flower: Quantitative approaches to computational vaccinology. Immunol. Cell Biol., 80(3), 270-279, 2002. [pdf]

8. Flower, D.R., I.A. Doytchinova: Immunoinformatics and the prediction of immunogenicity. Appl. Bioinformatics, 1(4), 167-176, 2002. [pdf]

9. Flower, D.R., I.A. Doytchinova, K. Paine, P. Taylor, M.J. Blythe, D. Lamponi, C. Zygouri, P. Guan, H. McSparron, H. Kirkbride: Computational Vaccine Design. In: Drug Design: Cutting Edge Approaches, (Ed. D.R. Flower), RSC publications, Cambridge, 136-180, 2002.

10. Aptula, A.O., Netzeva, T.I., Valkova, I.V., Cronin, M.T.D., Schultz, T.W., Kühne, R., Schüürmann, G,. Multivariate discrimination between modes of toxic action of phenols  Quantitative Structure-Activity Relationships 21 (1), 12-22, 2002.

11. Mitcheva, M., Vitcheva, V., Manolov, I., Valkova, I., Effects of two newly synthesized 4-hydroxycoumarin derivatives (4-OHC) on isolated rat hepatocytes   Methods and Findings in Experimental and Clinical Pharmacology 24 (6), 345-349, 2002.

12. Cronin, M.T.D., Aptula, A.O., Duffy, J.C., Netzeva, T.I., Rowe, P.H., Valkova, I.V., Schultz, T.W., Comparative assessment of methods to develop QSARs for the prediction of the toxicity of phenols to Tetrahymena pyriformis,  Chemosphere 49 (10), 1201-1221, 2002.




1. Doytchinova, I. CoMFA-Based Comparison of Two Models for Binding Site on Adenosine A1 receptors. J. Comput.-Aid. Mol. Des., 15, 2001, 1, 29-39.

2. Doytchinova, I., D.R.Flower. Towards the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity to class I MHC molecule HLA-A*0201. J. Med. Chem., 44, 2001, 3572-3581. [pdf]

3. Doytchinova, I., I. Valkova, R. Natcheva. CoMFA Study on Adenosine A2A Receptor Agonists. Quant. Struct. – Act. Relat., 20, 2001, 2, 124-129.




1. Netzeva, T., I. Doytchinova, R. Natcheva. 2D and 3D QSAR analysis of some valproic acid metabolites and analogues as anticonvulsant agents. Pharmaceut. Res., 17, 2000, 6, 727-732.

2. Dimitrova, B., I. Doytchinova, M. Zlatkova. Reversed-phase high-performance liquid chromatography for evaluating the distribution behavior of pharmaceutical substances in suppository base Witepsol H15-phosphate buffer system. J. Pharmaceut. Biomed. Anal., 23, 2000, 955-964.





1.     Heun, G., N.Lambov, A.Zlatkov, P.Peikov, I.Doytchinova, K.Gesheva. Biodegradable cross-linked prodrug of the bronchial dilator Vephylline: II. Kinetics and quantum chemical studies on the release mechanism. J. Control. Release, 58, 1999, 189-194.

2.     Hadjipavlou-Litina, D., A. Geronikaki, R. Mgonzo, I. Doytchinova. Thiazolyl-N-substituted amides: a group of effective anti inflammatory agents with potential for local anaesthetic properties. Synthesis, biological evaluation and a QSAR approach. Drug Develop. Res., 48, 1999, 53-60.

3.     Netzeva, T., R. Natcheva, I. Doytchinova. A QSAR Study of Some Ethers of Dihydroartemisinin as Antimalarial Agents. Pharmacia, Sofia, 46, 1999, 1, 5-10.




1.     Doytchinova, I. , S.Petrova. “N6-N7” - a Modification of the “N6-C8” Model for the Binding Site on Adenosine A1 Receptors with Improved Steric and Electrostatic Fit. Med.Chem.Res., 8, 1998, 3, 143-152.

2.     Netzeva, T., R.Natcheva, I.Doytchinova, I.Lesigiarska, D.Mihailova. Theoretical investigation of the chemical structure and QSAR-analysis of a series of 9-substituted artemisinin derivatives. Archives of the Balkan Medical Union , 33, 1998, 4, 189-198.





1.     Doytchinova, I. , R.Natcheva. QSAR-Study on a Series of 1,4-disubstituted Piperazines with Analgesic Activity. Acta Pharm., 47, 1997, 3, 189-195.




1.     Дойчинова, И., Р. Начева, Д. Михайлова. QSAR анализ на серия новосинтезирани производни на ксантина. Фармация, София, 43, 1995, 1, 8-12.

2.     Дойчинова, И., Р. Начева, Д. Михайлова. QSAR анализ на серия 3-пропилксантини с бронходилатиращо действие. Фармация, София, 43, 1995, 5-6, 30-36.




1.     Doichinova, I.A., R.N.Natcheva, D.N.Mihailova. QSAR-Studies of 8-Substituted Xanthines as Adenosine Receptors Antagonists. Eur. J. Med. Chem., 29, 1994, 2, 133-138.