Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB.

Mridula Sharma, Indra Kundu, Ram Shankar Barai, Sameeksha Bhaye, Karishma Desai, Khushal Pokar & Susan Idicula-Thomas
Sci Rep 11, 4203 (2021).

Exploring the druggable proteome of Candida species through comprehensive computational analysis

Shuvechha Mukherjeea, Indra Kundua, Mehdi Askari, Ram Shankar Barai, K.V.Venkatesh, Susan Idicula-Thomas
Genomics Volume 113, Issue 2, March 2021, Pages 728-739

A 5-mer peptide derived from hinge region of hFSHR can function as positive allosteric modulator in vivo

Prabhudesai KS, Aathi MS, Dighe V, Idicula-Thomas S
Biochimica et Biophysica Acta (BBA)-Biomembranes, 183492

PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome.

Sharma M, Barai RS, Kundu I, Bhaye S, Pokar K, Idicula-Thomas S
Sci Rep 10, 14738.  doi: 10.1038/s41598-020-71418-8

Identification and in vivo validation of a 9-mer peptide derived from FSHβ with FSHR antagonist activity

Prabhudesai KS, Raje S, Dhamanaskar A. Modi D. Dighe V. Contini A. Idicula-Thomas S.
Peptides. 2020;132:170367. doi:10.1016/j.peptides.2020.170367

A steady-state modeling approach for simulation of antimicrobial peptide-cell membrane interaction

Srinivasan S, Waghu FH, Idicula-Thomas S, Venkatesh KV.
Biochim Biophys Acta Biomembr. 2020;1862(4):183242. doi:10.1016/j.bbamem.2020.183242

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities

Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader G D
Computational and Structural Biotechnology Journal

A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity

Waghu FH, Gawde U, Gomatam A, Coutinho E, Idicula-Thomas S
Chem Biol Drug Des. 2020;10.1111/cbdd.13749. doi:10.1111/cbdd.13749

Collection of antimicrobial peptides database and its derivatives: Applications and beyond

Waghu FH, Idicula-Thomas S
Protein Sci. 2020 Jan;29(1):36-42. doi: 10.1002/pro.3714PMID: 31441165

Effect of diversity in gp41 membrane proximal external region of primary HIV-1 Indian subtype C sequences on interaction with broadly neutralizing antibodies 4E10 and 10E8

Sutar J, Padwal V, Sonawani A, Nagar V, Patil P, Kulkarni B, Hingankar N, Deshpande S, Idicula-Thomas S, Jagtap D, Bhattacharya J, Bandivdekar A, Patel V.
Virus Res. 2019 Nov;273:197763. doi: 10.1016/j.virusres.2019.197763.PMID: 31553924

Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms

Sahu B, Shah S, Prabhudesai K, Contini A, Idicula-Thomas S
J Mol Graph Model Jun;89:156-166. doi: 10.1016/j.jmgm.2019.02.001.PMID: 30897497

Designing Antibacterial Peptides with Enhanced Killing Kinetics

Waghu FH, Joseph S, Ghawali S, Martis EA, Madan T, Venkatesh KV, Idicula- Thomas S
Front Microbiol. 2018 Feb 23;9:325. doi: 10.3389/fmicb.2018.00325PMID: 29527201

Tubulin acetylation: A novel functional avenue for CDYL in sperm.

Parab S, Dalvi V, Mylavaram S, Kishore A, Idicula-Thomas S, Sonawane S, Parte P
Cytoskeleton (Hoboken). 2017 Jul 6. 
PMID: 28681565

Evaluation of 4-thiazolidinone derivatives as potential reverse transcriptase inhibitors against HIV-1 drug resistant strains.

Suryawanshi R, Jadhav S, Makwana N, Desai D, Chaturbhuj D, Sonawani A, Idicula-Thomas S, Murugesan V, Katti SB, Tripathy S, Paranjape R, Kulkarni S
Bioorg Chem. 2017 Apr;71:211-218. 
PMID: 28236450

Transcriptional regulation of follicle-stimulating hormone beta-subunit in marmoset by an alternate distal promoter.

Kutteyil SS, Pathak BR, Mahale SD
Gen Comp Endocrinol. 2017 May 15;246:331-336. 
PMID: 28062307

PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases.

Shende G, Haldankar H, Barai RS, Bharmal MH, Shetty V, Idicula-Thomas S
Bioinformatics. 2017 Mar 15;33(6):929-931. 
PMID: 28039165

Functional characterization of two naturally occurring mutations V221G and T449N in the follicle stimulating hormone receptor.

Banerjee AA, Achrekar SK, Joseph S, Pathak BR, Mahale SD
Mol Cell Endocrinol. 2017 Jan 15;440:69-79. 
PMID: 27889471

Purification and characterization of CRISP-3 from human seminal plasma and its real-time binding kinetics with PSP94.

Anklesaria JH, Pandya RR, Pathak BR, Mahale SD
J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Dec 15;1039:59-65. 
PMID: 27825912

Comparison of marmoset and human FSH using synthetic peptides of the beta-subunit L2 loop region and anti-peptide antibodies.

Kutteyil SS, Kulkarni BJ, Mojidra R, Joseph S, Pathak BR, Mahale SD
J Pept Sci. 2016 Jun;22(6):397-405. 
PMID: 27282136

Identification of CRISP2 from human sperm as PSP94-binding protein and generation of CRISP2-specific anti-peptide antibodies.

Anklesaria JH, Kulkarni BJ, Pathak BR, Mahale SD
J Pept Sci. 2016 Jun;22(6):383-90. 
PMID: 27161017

Leveraging family-specific signatures for AMP discovery and high-throughput annotation.

Waghu FH, Barai RS, Idicula-Thomas S
Sci Rep. 2016 Apr 19;6:24684. 
PMID: 27089856

A triad of telomerase, androgen receptor and early growth response 1 in prostate cancer cells.

Jacob S, Nayak S, Kakar R, Chaudhari UK, Joshi D, Vundinti BR, Fernandes G, Barai RS, Kholkute SD, Sachdeva G
Cancer Biol Ther. 2016 Apr 2;17(4):439-48. 
PMID: 27003515

Novel FSH receptor mutation in a case of spontaneous ovarian hyperstimulation syndrome with successful pregnancy outcome.

Chauhan AR, Prasad M, Chamariya S, Achrekar S, Mahale SD, Mittal K
J Hum Reprod Sci. 2015 Oct-Dec;8(4):230-3. 
PMID: 26752859

PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome.

Joseph S, Barai RS, Bhujbalrao R, Idicula-Thomas S
Nucleic Acids Res. 2016 Jan 4;44(D1):D1032-5. 
PMID: 26578565

CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides.

Waghu FH, Barai RS, Gurung P, Idicula-Thomas S
Nucleic Acids Res. 2016 Jan 4;44(D1):D1094-7. 
PMID: 26467475

Cysteine-rich secretory protein 3 plays a role in prostate cancer cell invasion and affects expression of PSA and ANXA1.

Pathak BR, Breed AA, Apte S, Acharya K, Mahale SD
Mol Cell Biochem. 2016 Jan;411(1-2):11-21. 
PMID: 26369530

The rs10993994 in the proximal MSMB promoter region is a functional polymorphism in Asian Indian subjects.

Mhatre DR, Mahale SD, Khatkhatay MI, Achrekar SK, Desai SS, Jagtap DD, Dhabalia JV, Tongaonkar HB, Dandekar SP, Varadkar AM
Springerplus. 2015 Jul 28;4:380. 
PMID: 26240778

Role of the Extracellular and Intracellular Loops of Follicle-Stimulating Hormone Receptor in Its Function.

Banerjee AA, Mahale SD
Front Endocrinol (Lausanne). 2015 Jul 17;6:110. 
PMID: 26236283

Expression of Bioactive Callithrix jacchus Follicle-Stimulating Hormone in Pichia pastoris.

Kutteyil SS, Pathak BR, Dighe RR, Mahale SD
Appl Biochem Biotechnol. 2015 May;176(2):399-411. 
PMID: 25805018

FSH receptor-specific residues L501 and I505 in extracellular loop 2 are essential for its function.

Banerjee AA, Dupakuntla M, Pathak BR, Mahale SD
J Mol Endocrinol. 2015 Jun;54(3):193-204. 
PMID: 25791375

Functional characterization of two naturally occurring mutations (Val514Ala and Ala575Val) in follicle-stimulating hormone receptor.

Desai SS, Achrekar SK, Sahasrabuddhe KA, Meharji PK, Desai SK, Mangoli VS, Mahale SD
J Clin Endocrinol Metab. 2015 Apr;100(4):E638-45. 
PMID: 25581598

Cervical cancer in Indian women reveals contrasting association among common sub-family of HLA class I alleles.

Gokhale P, Mania-Pramanik J, Sonawani A, Idicula-Thomas S, Kerkar S, Tongaonkar H, Chaudhari H, Warke H, Salvi V
Immunogenetics. 2014 Dec;66(12):683-91. 
PMID: 25267060

Surfactant protein D inhibits HIV-1 infection of target cells via interference with gp120-CD4 interaction and modulates pro-inflammatory cytokine production.

Pandit H, Gopal S, Sonawani A, Yadav AK, Qaseem AS, Warke H, Patil A, Gajbhiye R, Kulkarni V, Al-Mozaini MA, Idicula-Thomas S, Kishore U, Madan T
PLoS One. 2014 Jul 18;9(7):e102395. 
PMID: 25036364

Development of an ELISA for sPSP94 and utility of the sPSP94/sPSA ratio as a diagnostic indicator to differentiate between benign prostatic hyperplasia and prostate cancer.

Mhatre DR, Mahale SD, Khatkhatay MI, Desai SS, Jagtap DD, Dhabalia JV, Tongaonkar HB, Desai MP, Dandekar SP, Varadkar AM
Clin Chim Acta. 2014 Sep 25;436:256-62. 
PMID: 24952364

Phase 1 dose escalation study of rigosertib by 2-, 4-, or 8-hour infusion twice-weekly in patients with advanced cancer.

Advani SH, Achrekar SD, Doval DC, Raghunadharao D, Wilhelm FE, Acharya M
Indian J Cancer. 2014 Jan-Mar;51(1):40-4. 
PMID: 24947095

Androgen receptor as a regulator of ZEB2 expression and its implications in epithelial-to-mesenchymal transition in prostate cancer.

Jacob S, Nayak S, Fernandes G, Barai RS, Menon S, Chaudhari UK, Kholkute SD, Sachdeva G
Endocr Relat Cancer. 2014 May 8;21(3):473-86. 
PMID: 24812058

HPV16 E6 variants: frequency, association with HPV types and in silico analysis of the identified novel variants.

Gokhale PS, Sonawani A, Idicula-Thomas S, Kerkar S, Tongaonkar H, Mania-Pramanik J
J Med Virol. 2014 Jun;86(6):968-74. 
PMID: 24610458

Polymeric nanoparticle formulation of octapeptide (NP-OP): in vitro release and in vivo effect in common marmosets, Callithrix jacchus Linn.

Nandedkar TD, Sagvekar P, Thakur B, Navlakhe R, Chitnis S, Mahale SD, D’Souza S, Patel KD, Vavia PR
Indian J Exp Biol. 2013 Dec;51(12):1055-62.
PMID: 24579370

CAMP: Collection of sequences and structures of antimicrobial peptides.

Waghu FH, Gopi L, Barai RS, Ramteke P, Nizami B, Idicula-Thomas S
Nucleic Acids Res. 2014 Jan;42(Database issue):D1154-8. 
PMID: 24265220

Mutations and polymorphisms in FSH receptor: functional implications in human reproduction.

Desai SS, Roy BS, Mahale SD
Reproduction. 2013 Oct 23;146(6):R235-48. 
PMID: 24051057

Association of allelic combinations of FSHR gene polymorphisms with ovarian response.

Desai SS, Achrekar SK, Paranjape SR, Desai SK, Mangoli VS, Mahale SD
Reprod Biomed Online. 2013 Oct;27(4):400-6. 
PMID: 23953588

In silico study on binding specificity of gonadotropins and their receptors: design of a novel and selective peptidomimetic for human follicle stimulating hormone receptor.

Sonawani A, Niazi S, Idicula-Thomas S
PLoS One. 2013 May 20;8(5):e64475. 
PMID: 23700481

Effect of FSH receptor-binding inhibitor-8 on FSH-mediated granulosa cell signaling and proliferation.

Navalakhe RM, Jagtap DD, Nayak SU, Nandedkar TD, Mahale SD
Chem Biol Drug Des. 2013 Aug;82(2):178-88. 
PMID: 23601330

Prostate Secretory Protein of 94 amino acids (PSP94) binds to prostatic acid phosphatase (PAP) in human seminal plasma.

Anklesaria JH, Jagtap DD, Pathak BR, Kadam KM, Joseph S, Mahale SD
PLoS One. 2013;8(3):e58631. 
PMID: 23469287

A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis.

Wolfe LM, Veeraraghavan U, Idicula-Thomas S, Schurer S, Wennerberg K, Reynolds R, Besra GS, Dobos KM
Mol Cell Proteomics. 2013 Jun;12(6):1644-60. 
PMID: 23462205

Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.

Breed AA, Gomes A, Roy BS, Mahale SD, Pathak BR
Biochim Biophys Acta. 2013 Apr;1830(4):3019-29. 
PMID: 23375721

ClassAMP: a prediction tool for classification of antimicrobial peptides.

Joseph S, Karnik S, Nilawe P, Jayaraman VK, Idicula-Thomas S
IEEE/ACM Trans Comput Biol Bioinform. 2012 Sep-Oct;9(5):1535-8.
PMID: 22732690

Identification of novel mutations in HEXA gene in children affected with Tay Sachs disease from India.

Mistri M, Tamhankar PM, Sheth F, Sanghavi D, Kondurkar P, Patil S, Idicula-Thomas S, Gupta S, Sheth J
PLoS One. 2012;7(6):e39122. 
PMID: 22723944

Extracellular loop 2 in the FSH receptor is crucial for ligand mediated receptor activation.

Dupakuntla M, Pathak B, Roy BS, Mahale SD
Mol Cell Endocrinol. 2012 Oct 15;362(1-2):60-8. 
PMID: 22641019

Imatinib resistance due to a novel tri-nucleotide insertion in the SH2/C lobe interface of BCR/ABL kinase domain between position K357 and N358.

Vaidya S, Sonawani A, Idicula-Thomas S, Vundinti BR, Ghosh K
Leuk Res. 2012 May;36(5):e110-2. 
PMID: 22387050

Novel homozygous mutations in Desert hedgehog gene in patients with 46,XY complete gonadal dysgenesis and prediction of its structural and functional implications by computational methods.

Das DK, Sanghavi D, Gawde H, Idicula-Thomas S, Vasudevan L
Eur J Med Genet. 2011 Nov-Dec;54(6):e529-34. 
PMID: 21816240

Follicle-stimulating hormone receptor polymorphism (G-29A) is associated with altered level of receptor expression in Granulosa cells.

Desai SS, Achrekar SK, Pathak BR, Desai SK, Mangoli VS, Mangoli RV, Mahale SD
J Clin Endocrinol Metab. 2011 Sep;96(9):2805-12. 
PMID: 21752882

Is 37LRP cell surface receptor for PSP94?

Pathak BR, Jagtap DD, Mahale SD
Asian J Androl. 2011 Mar;13(2):347. 
PMID: 21102472

Anti-HSP90 autoantibodies in sera of infertile women identify a dominant, conserved epitope EP6 (380-389) of HSP90 beta protein.

Pires ES, Choudhury AK, Idicula-Thomas S, Khole VV
Reprod Biol Endocrinol. 2011 Jan 27;9:16. 
PMID: 21272367

ClotBase: a knowledgebase on proteins involved in blood coagulation.

Sonawani A, Nilawe P, Barai RS, Idicula-Thomas S
Blood. 2010 Aug 5;116(5):855-6. 
PMID: 20688969

Growth inhibition mediated by PSP94 or CRISP-3 is prostate cancer cell line specific.

Pathak BR, Breed AA, Nakhawa VH, Jagtap DD, Mahale SD
Asian J Androl. 2010 Sep;12(5):677-89. 
PMID: 21102472

Emerging roles for the FSH receptor adapter protein APPL1 and overlap of a putative 14-3-3tau interaction domain with a canonical G-protein interaction site.

Dias JA, Mahale SD, Nechamen CA, Davydenko O, Thomas RM, Ulloa-Aguirre A
Mol Cell Endocrinol. 2010 Nov 25;329(1-2):17-25. 
PMID: 20600589

Effect of high intratesticular estrogen on global gene expression and testicular cell number in rats.

Balasinor NH, D’Souza R, Nanaware P, Idicula-Thomas S, Kedia-Mokashi N, He Z, Dym M
Reprod Biol Endocrinol. 2010 Jun 23;8:72. 
PMID: 20573204

High-affinity binding of seminal plasma PSP94 to human immunoglobulin is through the Fab domain.

Jagtap DD, Modi DN, Kumar M, Pathak BR, Mahale SD
Biochim Biophys Acta. 2010 Sep;1804(9):1889-94. 
PMID: 20554063

Molecular basis of factor X deficiency cases from India.

Mota L, Shetty S, Idicula-Thomas S, Ghosh K
Haemophilia. 2010 Jul 1;16(4):693-7. 
PMID: 20331754

Follicle stimulating hormone receptor gene variants in women with primary and secondary amenorrhea.

Achrekar SK, Modi DN, Meherji PK, Patel ZM, Mahale SD
J Assist Reprod Genet. 2010 Jun;27(6):317-26. 
PMID: 20237833

Crystal structure of prostate secretory protein PSP94 shows an edge-to-edge association of two monomers to form a homodimer.

Kumar A, Jagtap DD, Mahale SD, Kumar M
J Mol Biol. 2010 Apr 9;397(4):947-56. 
PMID: 20184897

CAMP: a useful resource for research on antimicrobial peptides.

Thomas S, Karnik S, Barai RS, Jayaraman VK, Idicula-Thomas S
Nucleic Acids Res. 2010 Jan;38(Database issue):D774-80. 
PMID: 19923233

Accessibility of the extracellular loops of follicle stimulating hormone receptor and their role in hormone-receptor interaction.

Dupakuntla M, Mahale SD
Mol Cell Endocrinol. 2010 Feb 5;315(1-2):131-7. 
PMID: 19825393

Phenotypic and genotypic characterization of Factor VII deficiency patients from Western India.

Mota L, Shetty S, Idicula-Thomas S, Ghosh K
Clin Chim Acta. 2009 Nov;409(1-2):106-11. 
PMID: 19751712

Interaction of follicle-stimulating hormone (FSH) receptor binding inhibitor-8: a novel FSH-binding inhibitor, with FSH and its receptor.

Chitnis SS, Selvaakumar C, Jagtap DD, Barnwal RP, Chary KV, Mahale SD, Nandedkar TD
Chem Biol Drug Des. 2009 Jun;73(6):637-43. 
PMID: 19635055

Poor ovarian response to gonadotrophin stimulation is associated with FSH receptor polymorphism.

Achrekar SK, Modi DN, Desai SK, Mangoli VS, Mangoli RV, Mahale SD
Reprod Biomed Online. 2009 Apr;18(4):509-15.
PMID: 19400992

Hereditary basis of protein C deficiency (PCD) in thrombosis patients: first report from India.

Pai N, Shetty S, Idicula-Thomas S, Kulkarni B, Ghosh K
Thromb Haemost. 2009 Apr;101(4):785-7.
PMID: 19350130

Crystallization and preliminary X-ray diffraction analysis of human seminal plasma protein PSP94.

Kumar M, Jagtap DD, Mahale SD, Prashar V, Kumar A, Das A, Bihani SC, Ferrer JL, Hosur MV, Ramanadham M
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Apr 1;65(Pt 4):389-91.
PMID: 19342788

A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods.

Dubey S, Idicula-Thomas S, Anwaruddin M, Saravanan C, Varma RR, Maitra A
J Biomed Sci. 2009 Jan 8;16:3. 
PMID: 19272182

Characterization of peptide 20-30 of follicle stimulating hormone receptor as an antagonist of receptor activity: significance of charged residues.

Dupakuntla M, Ghosalkar JD, Mahale SD
Chem Biol Drug Des. 2009 Jan;73(1):108-14. 
PMID: 19152639

Granulosa cell apoptosis induced by a novel FSH binding inhibitory peptide from human ovarian follicular fluid.

Chitnis SS, Navlakhe RM, Shinde GC, Barve SJ, D’Souza S, Mahale SD, Nandedkar TD
J Histochem Cytochem. 2008 Nov;56(11):961-8. 
PMID: 18645207

Follicle-stimulating hormone receptor polymorphism (Thr307Ala) is associated with variable ovarian response and ovarian hyperstimulation syndrome in Indian women.

Achrekar SK, Modi DN, Desai SK, Mangoli VS, Mangoli RV, Mahale SD
Fertil Steril. 2009 Feb;91(2):432-9. 
PMID: 19732886

Effect of the human follicle-stimulating hormone-binding inhibitor and its N-terminal fragment on follicle-stimulating hormone-induced progesterone secretion by granulosa cells in vitro.

Wadia PR, Mahale SD, Nandedkar TD
J Biosci. 2007 Sep;32(6):1185-94.
PMID: 17954979

Correlation between the structural stability and aggregation propensity of proteins.

Idicula-Thomas S, Balaji PV
In Silico Biol. 2007;7(2):225-37.
PMID: 17688448

Disulphide bond reduction and S-carboxamidomethylation of PSP94 affects its conformation but not the ability to bind immunoglobulin.

Jagtap DD, Narahari A, Swamy MJ, Mahale SD
Biochim Biophys Acta. 2007 Jun;1774(6):723-31. Epub 2007 Apr 5.
PMID: 17493883

Identification of the region 285-309 of follicle stimulating hormone receptor as a bioneutralizing epitope.

Ghosalkar JD, Dharma SJ, Nandedkar TD, Mahale SD
J Reprod Immunol. 2007 Jun;74(1-2):24-33. Epub 2007 Feb 5.
PMID: 17280718

Detailed analysis of the region 9-30 of rat follicle stimulating hormone receptor: identification of peptide 20-30 as a potential hormone binding inhibitor.

Ghosalkar JD, Mahale SD
Peptides. 2006 Nov;27(11):2894-900. Epub 2006 Jul 25.
PMID: 16870304