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Chaudhary, Anita and Bhalla, Sherry and Patiyal, Sumeet and Raghava, G.P.S. and Sahni, Girish (2021) FermFooDb: A database of bioactive peptides derived from fermented foods. CELL PRESS.
Lathwal, Anjali and Kumar, Rajesh and Raghava, G.P.S. (2021) In-silico identification of subunit vaccine candidates against lung cancer-associated oncogenic viruses. Computers in Biology and Medicine, 130.
Lathwal, Anjali and Kumar, Rajesh and Raghava, G.P.S. (2020) OvirusTdb: A database of oncolytic viruses for the advancement of therapeutics in cancer. Virology, 548. pp. 109-116.
Lathwal, Anjali and Kumar, Rajesh and Arora, Chakit and Raghava, G.P.S. (2020) Identification of prognostic biomarkers for major subtypes of non-small-cell lung cancer using genomic and clinical data. JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY. (In Press)
Lathwal, Anjali and Kumar, Rajesh and Raghava, G.P.S. (2020) Computer-aided designing of oncolytic viruses for overcoming translational challenges of cancer immunotherapy. Drug discovery today. ISSN 1878-5832 (In Press)
Bhalla, Sherry and Kaur, Harpreet and Kaur, Rishemjit and Sharma, Suresh and Raghava, G.P.S. (2020) Expression based biomarkers and models to classify early and late-stage samples of Papillary Thyroid Carcinoma. PloS one, 15 (4). e0231629. ISSN 1932-6203
Dhall, Anjali and Patiyal, Sumeet and Kaur, Harpreet and Bhalla, Sherry and Arora, Chakit and Raghava, G.P.S. (2020) Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics. Frontiers in genetics, 11. p. 221. ISSN 1664-8021
Kaur, Harpreet and Dhall, Anjali and Kumar, Rajesh and Raghava, G.P.S. (2020) Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. Frontiers in genetics, 10. p. 1306. ISSN 1664-8021
Patiyal, Sumeet and Agrawal, Piyush and Kumar, Vinod and Dhall, Anjali and Kumar, Rajesh and Mishra, Gaurav and Raghava, G.P.S. (2020) NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence. Protein science : a publication of the Protein Society, 29 (1). pp. 201-210. ISSN 1469-896X
Kumar, Vinod and Kumar, Rajesh and Agrawal, Piyush and Patiyal, Sumeet and Raghava, G.P.S. (2020) A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure. Frontiers in pharmacology, 11. ISSN 1663-9812
Kumar, Rajesh and Patiyal, Sumeet and Kumar, Vinod and Nagpal, Gandharva and Raghava, G.P.S. (2019) In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. International journal of molecular sciences, 20 (14). ISSN 1422-0067
Kumar, Rajesh and Nagpal, Gandharva and Kumar, Vinod and Usmani, Salman Sadullah and Agrawal, Piyush and Raghava, G.P.S. (2019) HumCFS: a database of fragile sites in human chromosomes. BMC genomics, 19 (Supp 9). pp. 1-8. ISSN 1471-2164
Agrawal, Piyush and Singh, Harinder and Srivastava, Hemant Kumar and Singh, Sandeep and Kishore, Gaurav and Raghava, G.P.S. (2019) Benchmarking of different molecular docking methods for protein-peptide docking. BMC bioinformatics, 19 (Suppl ). p. 426. ISSN 1471-2105
Usmani, Salman Sadullah and Agrawal, Piyush and Sehgal, Manika and Patel, Pradeep Kumar and Raghava, G.P.S. (2019) ImmunoSPdb: an archive of immunosuppressive peptides. Database : the journal of biological databases and curation, 2019. ISSN 1758-0463
Kaur, Dilraj and Patiyal, Sumeet and Sharma, Neelam and Usmani, Salman Sadullah and Raghava, G.P.S. (2019) PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands. Database : the journal of biological databases and curation, 2019. ISSN 1758-0463
Usmani, Salman Sadullah and Bhalla, Sherry and Raghava, G.P.S. (2018) Prediction of Antitubercular Peptides From Sequence Information Using Ensemble Classifier and Hybrid Features. Frontiers in pharmacology, 9. p. 954. ISSN 1663-9812
Nagpal, Gandharva and Chaudhary, Kumardeep and Agrawal, Piyush and Raghava, G.P.S. (2018) Computer-aided prediction of antigen presenting cell modulators for designing peptide-based vaccine adjuvants. Journal of translational medicine, 16 (1). p. 181. ISSN 1479-5876
Mathur, Deepika and Singh, Sandeep and Mehta, Ayesha and Agrawal, Piyush and Raghava, G.P.S. (2018) In silico approaches for predicting the half-life of natural and modified peptides in blood. PloS one, 13 (6). e0196829. ISSN 1932-6203
Agrawal, Piyush and Bhalla, Sherry and Chaudhary, Kumardeep and Kumar, Rajesh and Sharma, Meenu and Raghava, G.P.S. (2018) In silco Approach for Prediction of Antifungal Peptides. Frontiers in microbiology, 9. p. 323. ISSN 1664-302X
Gupta, Dinesh and Mathur, Deepika and Mehta, Ayesha and Firmal, Priyanka and Bedi, Gursimran and Sood, Charu and Gautam, Ankur and Raghava, G.P.S. (2018) TopicalPdb: A database of topically delivered peptides. PLOS ONE, 13 (2). e0190134. ISSN 1932-6203
Usmani, Salman Sadullah and Kumar, Rajesh and Kumar, Vinod and Singh, Sandeep and Raghava, G.P.S. (2018) AntiTbPdb: a knowledgebase of anti-tubercular peptides. Database : the journal of biological databases and curation, 2018. ISSN 1758-0463
Usmani, Salman Sadullah and Kumar, Rajesh and Bhalla, Sherry and Kumar, Vinod and Raghava, G.P.S. (2018) In Silico Tools and Databases for Designing Peptide-Based Vaccine and Drugs. Advances in protein chemistry and structural biology, 112. pp. 221-263. ISSN 1876-1631
Baindara, Piyush and Gautam, Ankur and Raghava, G.P.S. and Korpole, Suresh (2017) Anticancer properties of a defensin like class IId bacteriocin Laterosporulin10. Scientific Reports, 7. p. 46541. ISSN 2045-2322
Bhalla, Sherry and Verma, Ruchi and Kaur, Harpreet and Kumar, Rajesh and Usmani, Salman Sadullah and Sharma, Suresh and Raghava, G.P.S. (2017) CancerPDF: A repository of cancer-associated peptidome found in human biofluids. Scientific Reports, 7 (1). ISSN 2045-2322
Nagpal, Gandharva and Chaudhary, Kumardeep and Dhanda, Sandeep Kumar and Raghava, G.P.S. (2017) Computational Prediction of the Immunomodulatory Potential of RNA Sequences. Methods Molecular Biology, 1632. pp. 75-90. ISSN 1064-3745
Nagpal, Gandharva and Usmani, Salman Sadullah and Dhanda, Sandeep Kumar and Kaur, Harpreet and Singh, Sandeep and Sharma, Meenu and Raghava, G.P.S. (2017) Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Scientific Reports, 7. p. 42851. ISSN 2045-2322
Bhalla, Sherry and Chaudhary, Kumardeep and Kumar, Ritesh and Sehgal, Manika and Kaur, Harpreet and Sharma, Suresh and Raghava, G.P.S. (2017) Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer. Scientific Reports, 7. ISSN 2045-2322
Ahmed, Niyaz and Pahil, Sapna and Taneja, Neelam and Ansari, Hifzur Rahman and Raghava, G.P.S. (2017) In silico analysis to identify vaccine candidates common to multiple serotypes of Shigella and evaluation of their immunogenicity. PLOS ONE, 12 (8). e0180505. ISSN 1932-6203
Sang, Qing-Xiang Amy and Usmani, Salman Sadullah and Bedi, Gursimran and Samuel, Jesse S. and Singh, Sandeep and Kalra, Sourav and Kumar, Pawan and Ahuja, Anjuman Arora and Sharma, Meenu and Gautam, Ankur and Raghava, G.P.S. (2017) THPdb: Database of FDA-approved peptide and protein therapeutics. PLOS ONE, 12 (7). e0181748. ISSN 1932-6203
Randhawa, Harmandeep Kaur and Gautam, Ankur and Sharma, Minakshi and Bhatia, Rakesh and Varshney, Grish C and Raghava, G.P.S. and Nandanwar, Hemraj (2016) Cell-penetrating peptide and antibiotic combination therapy: a potential alternative to combat drug resistance in methicillin-resistant Staphylococcus aureus. Applied microbiology and biotechnology, 100 (9). pp. 4073-4083. ISSN 1432-0614
Agrawal, Piyush and Bhalla, Sherry and Usmani, Salman Sadullah and Singh, Sandeep and Chaudhary, Kumardeep and Raghava, G.P.S. and Gautam, Ankur (2016) CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. Nucleic acids research, 44 (D1). D1098-103. ISSN 1362-4962
Singh, Sandeep and Chaudhary, Kumardeep and Dhanda, Sandeep Kumar and Bhalla, Sherry and Usmani, Salman Sadullah and Gautam, Ankur and Tuknait, Abhishek and Agrawal, Piyush and Mathur, Deepika and Raghava, G.P.S. (2016) SATPdb: a database of structurally annotated therapeutic peptides. Nucleic acids research, 44 (D1). D1119-26. ISSN 1362-4962
Singh, Harinder and Raghava, G.P.S. (2016) BLAST-based structural annotation of protein residues using Protein Data Bank. Biology direct, 11 (1). p. 4. ISSN 1745-6150
Gautam, Ankur and Chaudhary, Kumardeep and Kumar, Rahul and Gupta, Sudheer and Singh, Harinder and Raghava, G.P.S. (2016) Managing Drug Resistance in Cancer: Role of Cancer Informatics. Methods in molecular biology (Clifton, N.J.), 1395. pp. 299-312. ISSN 1940-6029
Dhanda, Sandeep Kumar and Usmani, Salman Sadullah and Agrawal, Piyush and Nagpal, Gandharva and Gautam, Ankur and Raghava, G.P.S. (2016) Novelin silicotools for designing peptide-based subunit vaccines and immunotherapeutics. Briefings in Bioinformatics. bbw025. ISSN 1467-5463
Mathur, Deepika and Prakash, Satya and Anand, Priya and Kaur, Harpreet and Agrawal, Piyush and Mehta, Ayesha and Kumar, Rajesh and Singh, Sandeep and Raghava, G.P.S. (2016) PEPlife: A Repository of the Half-life of Peptides. Scientific Reports, 6 (1). ISSN 2045-2322
Chaudhary, Kumardeep and Nagpal, Gandharva and Dhanda, Sandeep Kumar and Raghava, G.P.S. (2016) Prediction of Immunomodulatory potential of an RNA sequence for designing non-toxic siRNAs and RNA-based vaccine adjuvants. Scientific reports, 6. p. 20678. ISSN 2045-2322
Gupta, Sudheer and Chaudhary, Kumardeep and Kumar, Rahul and Gautam, Ankur and Nanda, Jagpreet Singh and Dhanda, Sandeep Kumar and Brahmachari, Samir Kumar and Raghava, G.P.S. (2016) Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine. Scientific reports, 6. p. 23857. ISSN 2045-2322
Nupur, L N U and Vats, Asheema and Dhanda, Sandeep Kumar and Raghava, G.P.S. and Pinnaka, Anil Kumar and Kumar, Ashwani (2016) ProCarDB: a database of bacterial carotenoids. BMC microbiology, 16. p. 96. ISSN 1471-2180
Chaudhary, Kumardeep and Kumar, Ritesh and Singh, Sandeep and Tuknait, Abhishek and Gautam, Ankur and Mathur, Deepika and Anand, Priya and Varshney, Grish C and Raghava, G.P.S. (2016) A Web Server and Mobile App for Computing Hemolytic Potency of Peptides. Scientific reports, 6. ISSN 2045-2322
Dhanda, Sandeep Kumar and Vir, Pooja and Singla, Deepak and Gupta, Sudheer and Kumar, Shailesh and Raghava, G.P.S. (2016) A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. PloS one, 11 (4). e0153771. ISSN 1932-6203
Gupta, Amit Kumar and Kaur, Karambir and Rajput, Akanksha and Dhanda, Sandeep Kumar and Sehgal, Manika and Khan, Md Shoaib and Monga, Isha and Dar, Showkat Ahmad and Singh, Sandeep and Nagpal, Gandharva and Usmani, Salman Sadullah and Thakur, Anamika and Kaur, Gazaldeep and Sharma, Shivangi and Bhardwaj, Aman and Qureshi, Abid and Raghava, G.P.S. and Kumar, Manoj (2016) ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis. Scientific reports, 6. p. 32713. ISSN 2045-2322
Singh, Harinder and Srivastava, Hemant Kumar and Raghava, G.P.S. (2016) A web server for analysis, comparison and prediction of protein ligand binding sites. Biology direct, 11 (1). p. 14. ISSN 1745-6150
Dhanda, Sandeep Kumar and Chaudhary, Kumardeep and Gupta, Sudheer and Brahmachari, Samir Kumar and Raghava, G.P.S. (2016) A web-based resource for designing therapeutics against Ebola Virus. Scientific reports, 6. p. 24782. ISSN 2045-2322
Bhatia, Rakesh and Gautam, Ankur and Gautam, Shailendra K and Mehta, Divya and Kumar, Vinod and Raghava, G.P.S. and Varshney, Grish C (2015) Assessment of SYBR green I dye-based fluorescence assay for screening antimalarial activity of cationic peptides and DNA intercalating agents. Antimicrobial agents and chemotherapy, 59 (5). pp. 2886-9. ISSN 1098-6596
Singh, Harinder and Singh, Sandeep and Raghava, G.P.S. (2015) In silico platform for predicting and initiating β-turns in a protein at desired locations. Proteins, 83 (5). pp. 910-21. ISSN 1097-0134
Panwar, Bharat and Raghava, G.P.S. (2015) Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides. Genomics, 105 (4). pp. 197-203. ISSN 1089-8646
Dhar, Jesmita and Chakrabarti, Pinak and Saini, Harpreet and Raghava, G.P.S. and Kishore, Raghuvansh (2015) ω-Turn: a novel β-turn mimic in globular proteins stabilized by main-chain to side-chain C−H···O interaction. Proteins, 83 (2). pp. 203-14. ISSN 1097-0134
Kumar, Ravi and Chaudhary, Kumardeep and Sharma, Minakshi and Nagpal, Gandharva and Chauhan, Jagat Singh and Singh, Sandeep and Gautam, Ankur and Raghava, G.P.S. (2015) AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides. Nucleic acids research, 43 (Databa). D956-62. ISSN 1362-4962
Tyagi, Atul and Tuknait, Abhishek and Anand, Priya and Gupta, Sudheer and Sharma, Minakshi and Mathur, Deepika and Joshi, Anshika and Singh, Sandeep and Gautam, Ankur and Raghava, G.P.S. (2015) CancerPPD: a database of anticancer peptides and proteins. Nucleic acids research, 43. D837-43. ISSN 1362-4962
Gautam, Ankur and Sharma, Minakshi and Vir, Pooja and Chaudhary, Kumardeep and Kapoor, Pallavi and Kumar, Rahul and Nath, Samir K and Raghava, G.P.S. (2015) Identification and characterization of novel protein-derived arginine-rich cell-penetrating peptides. European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft für Pharmazeutische Verfahrenstechnik e.V, 89. pp. 93-106. ISSN 1873-3441
Ettayapuram Ramaprasad, Azhagiya Singam and Singh, Sandeep and Raghava, G.P.S. and Venkatesan, Subramanian (2015) AntiAngioPred: A Server for Prediction of Anti-Angiogenic Peptides. PloS one, 10 (9). e0136990. ISSN 1932-6203
Gautam, Ankur and Chaudhary, Kumardeep and Kumar, Rahul and Raghava, G.P.S. (2015) Computer-Aided Virtual Screening and Designing of Cell-Penetrating Peptides. Methods in molecular biology (Clifton, N.J.), 1324. pp. 59-69. ISSN 1940-6029
Singh, Harinder and Gupta, Sudheer and Gautam, Ankur and Raghava, G.P.S. (2015) Designing B-Cell Epitopes for Immunotherapy and Subunit Vaccines. Methods in molecular biology (Clifton, N.J.), 1348. pp. 327-40. ISSN 1940-6029
Kumar, Rahul and Chauhan, Jagat Singh and Raghava, G.P.S. (2015) In Silico Designing and Screening of Antagonists against Cancer Drug Target XIAP. Current cancer drug targets, 15 (9). pp. 836-46. ISSN 1873-5576
Singh, Sandeep and Singh, Harinder and Tuknait, Abhishek and Chaudhary, Kumardeep and Singh, Balvinder and Kumaran, S and Raghava, G.P.S. (2015) PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biology direct, 10 (1). p. 73. ISSN 1745-6150
Gupta, Sudheer and Kapoor, Pallavi and Chaudhary, Kumardeep and Gautam, Ankur and Kumar, Rahul and Raghava, G.P.S. (2015) Peptide toxicity prediction. Methods in molecular biology (Clifton, N.J.), 1268. pp. 143-57. ISSN 1940-6029
Singh, Harinder and Kumar, Rahul and Singh, Sandeep and Chaudhary, Kumardeep and Gautam, Ankur and Raghava, G.P.S. (2015) Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines. BMC cancer, 16 (1). p. 77. ISSN 1471-2407
Singh, Harinder and Singh, Sandeep and Singla, Deepak and Agarwal, Subhash M and Raghava, G.P.S. (2015) QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random forest. Biology direct, 10. p. 10. ISSN 1745-6150
Singh, Sandeep and Chaudhary, Kumardeep and Dhanda, Sandeep Kumar and Bhalla, Sherry and Usmani, Salman Sadullah and Gautam, Ankur and Tuknait, Abhishek and Agrawal, Piyush and Mathur, Deepika and Raghava, G.P.S. (2015) SATPdb: a database of structurally annotated therapeutic peptides. Nucleic Acids Research, 44 (D1). D1119-D1126. ISSN 0305-1048
Nagpal, Gandharva and Gupta, Sudheer and Chaudhary, Kumardeep and Kumar Dhanda, Sandeep and Prakash, Satya and Raghava, G.P.S. (2015) VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants. Scientific Reports, 5. p. 12478. ISSN 2045-2322
Kumar, Ravi and Chaudhary, Kumardeep and Singh Chauhan, Jagat and Nagpal, Gandharva and Kumar, Rahul and Sharma, Minakshi and Raghava, G.P.S. (2015) An in silico platform for predicting, screening and designing of antihypertensive peptides. Scientific Reports, 5. p. 12512. ISSN 2045-2322
Kumar, Ravi and Chaudhary, Kumardeep and Sharma, Minakshi and Nagpal, Gandharva and Chauhan, Jagat Singh and Singh, Sandeep and Gautam, Ankur and Raghava, G.P.S. (2014) AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides. Nucleic acids research, 43. D956-62. ISSN 1362-4962
Gautam, Ankur and Chaudhary, Kumardeep and Singh, Sandeep and Joshi, Anshika and Anand, Priya and Tuknait, Abhishek and Mathur, Deepika and Varshney, Grish C and Raghava, G.P.S. (2014) Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides. Nucleic acids research, 42 (Databa). D444-9. ISSN 1362-4962
Sharma, Arun and Singla, Deepak and Rashid, Mamoon and Raghava, G.P.S. (2014) Designing of peptides with desired half-life in intestine-like environment. BMC bioinformatics, 15. p. 282. ISSN 1471-2105
Kumar, Rahul and Chaudhary, Kumardeep and Singla, Deepak and Gautam, Ankur and Raghava, G.P.S. (2014) Designing of promiscuous inhibitors against pancreatic cancer cell lines. Scientific reports, 4. p. 4668. ISSN 2045-2322
Yadav, Inderjit S and Singh, Harinder and Khan, Mohd Imran and Chaudhury, Ashok and Raghava, G.P.S. and Agarwal, Subhash M (2014) EGFRIndb: epidermal growth factor receptor inhibitor database. Anti-cancer agents in medicinal chemistry, 14 (7). pp. 928-35. ISSN 1875-5992
Singh, Harinder and Singh, Sandeep and Raghava, G.P.S. (2014) Evaluation of protein dihedral angle prediction methods. PloS one, 9 (8). e105667. ISSN 1932-6203
Ahmad, Sahil and Gupta, Sudheer and Kumar, Rahul and Varshney, Grish C and Raghava, G.P.S. (2014) Herceptin resistance database for understanding mechanism of resistance in breast cancer patients. Scientific reports, 4. p. 4483. ISSN 2045-2322
Nagpal, Gandharva and Sharma, Minakshi and Kumar, Shailesh and Chaudhary, Kumardeep and Gupta, Sudheer and Gautam, Ankur and Raghava, G.P.S. (2014) PCMdb: pancreatic cancer methylation database. Scientific reports, 4. p. 4197. ISSN 2045-2322
Panwar, Bharat and Arora, Amit and Raghava, G.P.S. (2014) Prediction and classification of ncRNAs using structural information. BMC genomics, 15. p. 127. ISSN 1471-2164
Panwar, Bharat and Raghava, G.P.S. (2014) Prediction of uridine modifications in tRNA sequences. BMC bioinformatics, 15. p. 326. ISSN 1471-2105
Chauhan, Jagat Singh and Dhanda, Sandeep Kumar and Singla, Deepak and Agarwal, Subhash M and Raghava, G.P.S. (2014) QSAR-based models for designing quinazoline/imidazothiazoles/pyrazolopyrimidines based inhibitors against wild and mutant EGFR. PloS one, 9 (7). e101079. ISSN 1932-6203
Gautam, A and Kapoor, P and Chaudhary, K and Kumar, R and Raghava, G.P.S. (2014) Tumor homing peptides as molecular probes for cancer therapeutics, diagnostics and theranostics. Current medicinal chemistry, 21 (21). pp. 2367-91. ISSN 1875-533X
Dhanda, Sandeep Kumar and Vir, Pooja and Raghava, G.P.S. (2013) Designing of interferon-gamma inducing MHC class-II binders. Biology direct, 8. p. 30. ISSN 1745-6150
Dhanda, Sandeep Kumar and Singla, Deepak and Mondal, Alok K and Raghava, G.P.S. (2013) DrugMint: a webserver for predicting and designing of drug-like molecules. Biology direct, 8. p. 28. ISSN 1745-6150
Gupta, Sudheer and Ansari, Hifzur Rahman and Gautam, Ankur and Raghava, G.P.S. (2013) Identification of B-cell epitopes in an antigen for inducing specific class of antibodies. Biology direct, 8. p. 27. ISSN 1745-6150
Tyagi, Atul and Kapoor, Pallavi and Kumar, Rahul and Chaudhary, Kumardeep and Gautam, Ankur and Raghava, G.P.S. (2013) In silico models for designing and discovering novel anticancer peptides. Scientific reports, 3. p. 2984. ISSN 2045-2322
Gupta, Sudheer and Kapoor, Pallavi and Chaudhary, Kumardeep and Gautam, Ankur and Kumar, Rahul and Raghava, G.P.S. (2013) In silico approach for predicting toxicity of peptides and protein. PloS one, 8 (9). e73957. ISSN 1932-6203
Kumar, Shailesh and Vikram, Surendra and Raghava, G.P.S. (2013) Genome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes. PloS one, 8 (8). e70624. ISSN 1932-6203
Bhartiya, Deeksha and Pal, Koustav and Ghosh, Sourav and Kapoor, Shruti and Jalali, Saakshi and Panwar, Bharat and Jain, Sakshi and Sati, Satish and Sengupta, Shantanu and Sachidanandan, Chetana and Raghava, G.P.S. and Sivasubbu, Sridhar and Scaria, Vinod (2013) lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database : the journal of biological databases and curation, 2013. ISSN 1758-0463
Singh, Harinder and Ansari, Hifzur Rahman and Raghava, G.P.S. (2013) Improved method for linear B-cell epitope prediction using antigen's primary sequence. PloS one, 8 (5). e62216. ISSN 1932-6203
Singla, Deepak and Dhanda, Sandeep Kumar and Chauhan, Jagat S and Bhardwaj, Anshu and Brahmachari, Samir K and Raghava, G.P.S. (2013) Open source software and web services for designing therapeutic molecules. Current topics in medicinal chemistry, 13 (10). pp. 1172-91. ISSN 1873-4294
Vikram, Surendra and Kumar, Shailesh and Vaidya, Bhumika and Pinnaka, Anil Kumar and Raghava, G.P.S. (2013) Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon. Genome announcements, 1 (2). e00058-13. ISSN 2169-8287
Panwar, Bharat and Gupta, Sudheer and Raghava, G.P.S. (2013) Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information. BMC bioinformatics, 14. p. 44. ISSN 1471-2105
Kumar, Shailesh and Kaur, Chandandeep and Kimura, Kazuyuki and Takeo, Masahiro and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of the Type Species of the Genus Citrobacter, Citrobacter freundii MTCC 1658. Genome announcements, 1 (1). ISSN 2169-8287
Singh, Shoor Vir and Kumar, Naveen and Singh, Shree Narayan and Bhattacharya, Tapas and Sohal, Jagdip Singh and Singh, Pravin Kumar and Singh, Ajay Vir and Singh, Brajesh and Chaubey, Kundan Kumar and Gupta, Saurabh and Sharma, Nitu and Kumar, Shailesh and Raghava, G.P.S. (2013) Genome Sequence of the "Indian Bison Type" Biotype of Mycobacterium avium subsp. paratuberculosis Strain SS. Genome announcements, 1 (1). ISSN 2169-8287
Mangal, Manu and Sagar, Parul and Singh, Harinder and Raghava, G.P.S. and Agarwal, Subhash M (2013) NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database. Nucleic acids research, 41 (Databa). D1124-9. ISSN 1362-4962
Singla, Deepak and Tewari, Rupinder and Kumar, Ashwani and Raghava, G.P.S. (2013) Designing of inhibitors against drug tolerant Mycobacterium tuberculosis (H37Rv). Chemistry Central journal, 7 (1). p. 49. ISSN 1752-153X
Singh, Nitin Kumar and Kumar, Shailesh and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of Acinetobacter baumannii Strain MSP4-16. Genome announcements, 1 (2). e0013713. ISSN 2169-8287
Kaur, Navjot and Kumar, Shailesh and Bala, Monu and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T. Genome announcements, 1 (2). e0013813. ISSN 2169-8287
Bala, Monu and Kumar, Shailesh and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of Rhodococcus ruber Strain BKS 20-38. Genome announcements, 1 (2). e0013913. ISSN 2169-8287
Kumar, Shailesh and Bala, Monu and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14. Genome announcements, 1 (2). e0012913. ISSN 2169-8287
Kumar, Shailesh and Kaur, Navjot and Singh, Nitin Kumar and Raghava, G.P.S. and Mayilraj, Shanmugam (2013) Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. Genome announcements, 1 (2). ISSN 2169-8287
Vikram, Surendra and Pandey, Janmejay and Kumar, Shailesh and Raghava, G.P.S. (2013) Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98. PloS one, 8 (12). e84766. ISSN 1932-6203
Kumar, Ravi and Raghava, G.P.S. (2013) Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence. PloS one, 8 (4). e61437. ISSN 1932-6203
Gautam, Ankur and Chaudhary, Kumardeep and Kumar, Rahul and Sharma, Arun and Kapoor, Pallavi and Tyagi, Atul and Raghava, G.P.S. (2013) In silico approaches for designing highly effective cell penetrating peptides. Journal of translational medicine, 11. p. 74. ISSN 1479-5876
Ansari, Hifzur Rahman and Raghava, G.P.S. (2013) In silico models for B-cell epitope recognition and signaling. Methods in molecular biology (Clifton, N.J.), 993. pp. 129-38. ISSN 1940-6029
Chauhan, Jagat Singh and Rao, Alka and Raghava, G.P.S. (2013) In silico platform for prediction of N-, O- and C-glycosites in eukaryotic protein sequences. PloS one, 8 (6). e67008. ISSN 1932-6203
Mangal, Manu and Sagar, Parul and Singh, Harinder and Raghava, G.P.S. and Agarwal, Subhash M (2012) NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database. Nucleic acids research, 41 (D1). D1124-D1129. ISSN 1362-4962
Kumar, Shailesh and Kushwaha, Hariom and Bachhawat, Anand K and Raghava, G.P.S. and Ganesan, K (2012) Genome sequence of the oleaginous red yeast Rhodosporidium toruloides MTCC 457. Eukaryotic cell, 11 (8). pp. 1083-4. ISSN 1535-9786
Kumar, Shailesh and Randhawa, Anmoldeep and Ganesan, K and Raghava, G.P.S. and Mondal, Alok K (2012) Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234. Eukaryotic cell, 11 (7). pp. 961-2. ISSN 1535-9786
Vikram, Surendra and Kumar, Shailesh and Subramanian, Srikrishna and Raghava, G.P.S. (2012) Draft genome sequence of the nitrophenol-degrading actinomycete Rhodococcus imtechensis RKJ300. Journal of bacteriology, 194 (13). p. 3543. ISSN 1098-5530
Kumar, Shailesh and Vikram, Surendra and Subramanian, Srikrishna and Raghava, G.P.S. and Pinnaka, Anil Kumar (2012) Genome sequence of the halotolerant bacterium Imtechella halotolerans K1T. Journal of bacteriology, 194 (14). p. 3731. ISSN 1098-5530
Kumar, Shailesh and Subramanian, Srikrishna and Raghava, G.P.S. and Pinnaka, Anil Kumar (2012) Genome sequence of the marine bacterium Marinilabilia salmonicolor JCM 21150T. Journal of bacteriology, 194 (14). p. 3746. ISSN 1098-5530
Kumar, Shailesh and Vikram, Surendra and Raghava, G.P.S. (2012) Genome sequence of the nitroaromatic compound-degrading Bacterium Burkholderia sp. strain SJ98. Journal of bacteriology, 194 (12). p. 3286. ISSN 1098-5530
Panwar, Bharat and Raghava, G.P.S. (2012) Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino acids, 42 (5). pp. 1703-13. ISSN 1438-2199
Singh, Harinder and Chauhan, Jagat S and Gromiha, M Michael and Raghava, G.P.S. (2012) ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic acids research, 40 (Databa). D486-9. ISSN 1362-4962
Vikram, Surendra and Pandey, Janmejay and Bhalla, Nidhi and Pandey, Gunjan and Ghosh, Anuradha and Khan, Fazlurrahman and Jain, R K and Raghava, G.P.S. (2012) Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster. AMB Express, 2 (1). p. 30. ISSN 2191-0855
Gautam, Ankur and Singh, Harinder and Tyagi, Atul and Chaudhary, Kumardeep and Kumar, Rahul and Kapoor, Pallavi and Raghava, G.P.S. (2012) CPPsite: a curated database of cell penetrating peptides. Database : the journal of biological databases and curation, 2012. bas015. ISSN 1758-0463
Chauhan, Jagat S and Bhat, Adil H and Raghava, G.P.S. and Rao, Alka (2012) GlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences. PloS one, 7 (7). e40155. ISSN 1932-6203
Aithal, Abhijit and Sharma, Arun and Joshi, Shilpy and Raghava, G.P.S. and Varshney, Grish C (2012) PolysacDB: a database of microbial polysaccharide antigens and their antibodies. PloS one, 7 (4). e34613. ISSN 1932-6203
Bhat, Aadil H and Mondal, Homchoru and Chauhan, Jagat S and Raghava, G.P.S. and Methi, Amrish and Rao, Alka (2012) ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins. Nucleic acids research, 40 (D1). D388-D393. ISSN 1362-4962
Kapoor, Pallavi and Singh, Harinder and Gautam, Ankur and Chaudhary, Kumardeep and Kumar, Rahul and Raghava, G.P.S. (2012) TumorHoPe: a database of tumor homing peptides. PloS one, 7 (4). e35187. ISSN 1932-6203
Zhang, Guang Lan and Ansari, Hifzur Rahman and Bradley, Phil and Cawley, Gavin C and Hertz, Tomer and Hu, Xihao and Jojic, Nebojsa and Kim, Yohan and Kohlbacher, Oliver and Lund, Ole and Lundegaard, Claus and Magaret, Craig A and Nielsen, Morten and Papadopoulos, Harris and Raghava, G.P.S. and Tal, Vider-Shalit and Xue, Li C and Yanover, Chen and Zhu, Shanfeng and Rock, Michael T and Crowe, James E and Panayiotou, Christos and Polycarpou, Marios M and Duch, Włodzisław and Brusic, Vladimir (2011) Machine learning competition in immunology - Prediction of HLA class I binding peptides. Journal of immunological methods, 374 (1-2). pp. 1-4. ISSN 1872-7905
Bhardwaj, Anshu and Scaria, Vinod and Raghava, G.P.S. and Lynn, Andrew Michael and Chandra, Nagasuma and Banerjee, Sulagna and Raghunandanan, Muthukurussi V and Pandey, Vikas and Taneja, Bhupesh and Yadav, Jyoti and Dash, Debasis and Bhattacharya, Jaijit and Misra, Amit and Kumar, Anil and Ramachandran, Srinivasan and Thomas, Zakir and Brahmachari, Samir K (2011) Open source drug discovery- A new paradigm of collaborative research in tuberculosis drug development. Tuberculosis (Edinburgh, Scotland), 91 (5). pp. 479-86. ISSN 1873-281X
Panwar, Bharat and Raghava, G.P.S. (2011) Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino acids. ISSN 1438-2199
Kumar, Ravi and Panwar, Bharat and Chauhan, Jagat S and Raghava, G.P.S. (2011) Analysis and prediction of cancerlectins using evolutionary and domain information. BMC research notes, 4. p. 237. ISSN 1756-0500
Ahmed, Firoz and Raghava, G.P.S. (2011) Designing of highly effective complementary and mismatch siRNAs for silencing a gene. PloS one, 6 (8). e23443. ISSN 1932-6203
Tyagi, Atul and Ahmed, Firoz and Thakur, Nishant and Sharma, Arun and Raghava, G.P.S. and Kumar, Manoj (2011) HIVsirDB: A Database of HIV Inhibiting siRNAs. PloS one, 6 (10). e25917. ISSN 1932-6203
Agarwal, Sandhya and Mishra, Nitish K and Singh, Harinder and Raghava, G.P.S. (2011) Identification of mannose interacting residues using local composition. PloS one, 6 (9). e24039. ISSN 1932-6203
Kumar, Manish and Gromiha, M Michael and Raghava, G.P.S. (2011) SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. Journal of molecular recognition : JMR, 24 (2). pp. 303-13. ISSN 1099-1352
Singla, Deepak and Anurag, Meenakshi and Dash, Debasis and Raghava, G.P.S. (2011) A web server for predicting inhibitors against bacterial target GlmU protein. BMC pharmacology, 11. p. 5. ISSN 1471-2210
Rashid, Mamoon and Ramasamy, Sumathy and Raghava, G.P.S. (2010) A simple approach for predicting protein-protein interactions. Current protein & peptide science, 11 (7). pp. 589-600. ISSN 1875-5550
Verma, Ruchi and Varshney, Grish C and Raghava, G.P.S. (2010) Prediction of mitochondrial proteins of malaria parasite using split amino acid composition and PSSM profile. Amino acids, 39 (1). pp. 101-10. ISSN 1438-2199
Ansari, Hifzur Rahman and Raghava, G.P.S. (2010) Identification of NAD interacting residues in proteins. BMC bioinformatics, 11. p. 160. ISSN 1471-2105
Ansari, Hifzur Rahman and Flower, Darren R and Raghava, G.P.S. (2010) AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic acids research, 38 (Databa). D847-53. ISSN 1362-4962
Lata, Sneh and Mishra, Nitish K and Raghava, G.P.S. (2010) AntiBP2: improved version of antibacterial peptide prediction. BMC bioinformatics, 11 Sup. S19. ISSN 1471-2105
Singla, Deepak and Sharma, Arun and Kaur, Jasjit and Panwar, Bharat and Raghava, G.P.S. (2010) BIAdb: a curated database of benzylisoquinoline alkaloids. BMC pharmacology, 10. p. 4. ISSN 1471-2210
Pashov, Anastas and Monzavi-Karbassi, Behjatolah and Raghava, G.P.S. and Kieber-Emmons, Thomas (2010) Bridging innate and adaptive antitumor immunity targeting glycans. Journal of biomedicine & biotechnology, 2010. p. 354068. ISSN 1110-7251
Ansari, Hifzur Rahman and Raghava, G.P.S. (2010) Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome research, 6. p. 6. ISSN 1745-7580
Garg, Aarti and Tewari, Rupinder and Raghava, G.P.S. (2010) KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials. BMC bioinformatics, 11. p. 125. ISSN 1471-2105
Panwar, Bharat and Raghava, G.P.S. (2010) Prediction and classification of aminoacyl tRNA synthetases using PROSITE domains. BMC genomics, 11. p. 507. ISSN 1471-2164
Mishra, Nitish K and Raghava, G.P.S. (2010) Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information. BMC bioinformatics, 11 Sup. S48. ISSN 1471-2105
Chauhan, Jagat S and Mishra, Nitish K and Raghava, G.P.S. (2010) Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information. BMC bioinformatics, 11. p. 301. ISSN 1471-2105
Mishra, Nitish K and Agarwal, Sandhya and Raghava, G.P.S. (2010) Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule. BMC pharmacology, 10. p. 8. ISSN 1471-2210
Garg, Aarti and Tewari, Rupinder and Raghava, G.P.S. (2010) Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis. BMC bioinformatics, 11 Sup. S53. ISSN 1471-2105
Chaudhary, Neelkamal and Mahajan, Lakshna and Madan, Taruna and Kumar, Anil and Raghava, G.P.S. and Katti, Seturam Bandacharya and Haq, Wahajul and Sarma, Puranam Usha (2009) Prophylactic and Therapeutic Potential of Asp f1 Epitopes in Naïve and Sensitized BALB/c Mice. Immune network, 9 (5). pp. 179-91. ISSN 2092-6685
Lata, Sneh and Raghava, G.P.S. (2009) Prediction and classification of chemokines and their receptors. Protein engineering, design & selection : PEDS, 22 (7). pp. 441-4. ISSN 1741-0134
Kaundal, Rakesh and Raghava, G.P.S. (2009) RSLpred: an integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information. Proteomics, 9 (9). pp. 2324-42. ISSN 1615-9861
Rashid, Mamoon and Singla, Deepak and Sharma, Arun and Kumar, Manish and Raghava, G.P.S. (2009) Hmrbase: a database of hormones and their receptors. BMC genomics, 10. p. 307. ISSN 1471-2164
Chauhan, Jagat S and Mishra, Nitish K and Raghava, G.P.S. (2009) Identification of ATP binding residues of a protein from its primary sequence. BMC bioinformatics, 10. p. 434. ISSN 1471-2105
Lata, Sneh and Bhasin, Manoj and Raghava, G.P.S. (2009) MHCBN 4.0: A database of MHC/TAP binding peptides and T-cell epitopes. BMC research notes, 2. p. 61. ISSN 1756-0500
Arora, Pankaj Kumar and Kumar, Manish and Chauhan, Archana and Raghava, G.P.S. and Jain, R K (2009) OxDBase: a database of oxygenases involved in biodegradation. BMC research notes, 2. p. 67. ISSN 1756-0500
Ahmed, Firoz and Ansari, Hifzur Rahman and Raghava, G.P.S. (2009) Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC bioinformatics, 10. p. 105. ISSN 1471-2105
Kumar, Manish and Raghava, G.P.S. (2009) Prediction of nuclear proteins using SVM and HMM models. BMC bioinformatics, 10. p. 22. ISSN 1471-2105
Ahmed, Firoz and Kumar, Manish and Raghava, G.P.S. (2009) Prediction of polyadenylation signals in human DNA sequences using nucleotide frequencies. In silico biology, 9 (3). pp. 135-48. ISSN 1386-6338
Sethi, Deepti and Garg, Aarti and Raghava, G.P.S. (2008) DPROT: prediction of disordered proteins using evolutionary information. Amino acids, 35 (3). pp. 599-605. ISSN 1438-2199
Lata, Sneh and Raghava, G.P.S. (2008) PRRDB: a comprehensive database of pattern-recognition receptors and their ligands. BMC genomics, 9. p. 180. ISSN 1471-2164
Vivona, Sandro and Gardy, Jennifer L and Ramachandran, Srinivasan and Brinkman, Fiona S L and Raghava, G.P.S. and Flower, Darren R and Filippini, Francesco (2008) Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends in biotechnology, 26 (4). pp. 190-200. ISSN 0167-7799
Lata, Sneh and Raghava, G.P.S. (2008) CytoPred: a server for prediction and classification of cytokines. Protein engineering, design & selection : PEDS, 21 (4). pp. 279-282. ISSN 1741-0126
Kumar, Manish and Gromiha, M Michael and Raghava, G.P.S. (2008) Prediction of RNA binding sites in a protein using SVM and PSSM profile. Proteins, 71 (1). pp. 189-94. ISSN 1097-0134
Kush, Amit and Raghava, G.P.S. (2008) AC2Dgel: Analysis and Comparison of 2D gels. Journal of Proteomics & Bioinformatics, 1 (1). ISSN 0974276X
Kumar, Manish and Thakur, Varun and Raghava, G.P.S. (2008) COPid: composition based protein identification. In silico biology, 8 (2). pp. 121-8. ISSN 1386-6338
Kalita, Mridul K and Nandal, Umesh K and Pattnaik, Ansuman and Sivalingam, Anandhan and Ramasamy, Gowthaman and Kumar, Manish and Raghava, G.P.S. and Gupta, D (2008) CyclinPred: a SVM-based method for predicting cyclin protein sequences. PloS one, 3 (7). e2605. ISSN 1932-6203
Garg, Aarti and Raghava, G.P.S. (2008) ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins. BMC bioinformatics, 9. p. 503. ISSN 1471-2105
Verma, Ruchi and Tiwari, Ajit and Kaur, Sukhwinder and Varshney, Grish C and Raghava, G.P.S. (2008) Identification of proteins secreted by malaria parasite into erythrocyte using SVM and PSSM profiles. BMC bioinformatics, 9. pp. 1-11. ISSN 1471-2105
Garg, Aarti and Raghava, G.P.S. (2008) A machine learning based method for the prediction of secretory proteins using amino acid composition, their order and similarity-search. In silico biology, 8 (2). pp. 129-40. ISSN 1386-6338
Muthukrishnan, S and Garg, Aarti and Raghava, G.P.S. (2007) Oxypred: prediction and classification of oxygen-binding proteins. Genomics, proteomics & bioinformatics / Beijing Genomics Institute, 5 (3-4). pp. 250-2. ISSN 1672-0229
Bhasin, Manoj and Raghava, G.P.S. (2007) A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. Journal of biosciences, 32 (1). pp. 31-42. ISSN 0250-5991
Lata, Sneh and Sharma, B K and Raghava, G.P.S. (2007) Analysis and prediction of antibacterial peptides. BMC bioinformatics, 8. p. 263. ISSN 1471-2105
Lata, Sneh and Sharma, B K and Raghava, G.P.S. (2007) Analysis and prediction of antibacterial peptides. Nature Protocols. ISSN 2043-0116
Lata, Sneh and Bhasin, Manoj and Raghava, G.P.S. (2007) Application of machine learning techniques in predicting MHC binders. Methods in molecular biology (Clifton, N.J.), 409. pp. 201-15. ISSN 1064-3745
Saha, Sudipto and Raghava, G.P.S. (2007) BTXpred: prediction of bacterial toxins. In silico biology, 7 (4-5). pp. 405-412. ISSN 1386-6338
Kumar, Manish and Gromiha, M Michael and Raghava, G.P.S. (2007) Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC bioinformatics, 8. p. 463. ISSN 1471-2105
Kumar, Manish and Verma, Ruchi and Raghava, G.P.S. (2007) Mitpred2: an improved method for predicting mitochondrial proteins using SVM and HMM. Nature Protocols. ISSN 2043-0116
Kaur, Harpreet and Garg, Aarti and Raghava, G.P.S. (2007) PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein and peptide letters, 14 (7). pp. 626-31. ISSN 0929-8665
Pashov, Anastas and Monzavi-Karbassi, Behjatolah and Raghava, G.P.S. and Kieber-Emmons, Thomas (2007) Peptide mimotopes as prototypic templates of broad-spectrum surrogates of carbohydrate antigens for cancer vaccination. Critical reviews in immunology, 27 (3). pp. 247-70. ISSN 1040-8401
Saha, Sudipto and Raghava, G.P.S. (2007) Predicting virulence factors of immunological interest. Methods in molecular biology (Clifton, N.J.), 409. pp. 407-15. ISSN 1064-3745
Singh, Harpreet and Raghava, G.P.S. (2007) Prediction and mapping of promiscuous MHC class II binders in an antigen sequence. Nature Protocols. ISSN 2043-0116
Saha, Sudipto and Raghava, G.P.S. (2007) Prediction methods for B-cell epitopes. Methods in molecular biology (Clifton, N.J.), 409. pp. 387-94. ISSN 1064-3745
Saha, Sudipto and Raghava, G.P.S. (2007) Prediction of allergenic proteins and mapping of IgE epitopes in allergens. Natute Pritocols. ISSN 2043-0116
Saha, Sudipto and Raghava, G.P.S. (2007) Prediction of neurotoxins based on their function and source. In silico biology, 7 (4-5). pp. 369-87. ISSN 1386-6338
Raghava, G.P.S. (2007) Prediction of subcellular localization of proteins using machine learning techniques and evolutionary information. Amino acids, 33. x-xi. ISSN 1438-2199
Saha, Sudipto and Raghava, G.P.S. (2007) Searching and mapping of B-cell epitopes in Bcipep database. Methods in molecular biology (Clifton, N.J.), 409 (6). pp. 113-124. ISSN 1064-3745
Bhasin, Manoj and Lata, Sneh and Raghava, G.P.S. (2007) Searching and mapping of T-cell epitopes, MHC binders, and TAP binders. Methods in molecular biology (Clifton, N.J.), 409. pp. 95-112. ISSN 1064-3745
Srivastava, Shilpy and Singh, Mahender Kumar and Raghava, G.P.S. and Varshney, Grish C (2007) Searching haptens, carrier proteins, and anti-hapten antibodies. Methods in molecular biology (Clifton, N.J.), 409. pp. 125-39. ISSN 1064-3745
Rashid, Mamoon and Saha, Sudipto and Raghava, G.P.S. (2007) Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs. BMC bioinformatics Vol.8; 2007, 8. p. 337. ISSN 1471-2105
Mishra, Nitish K and Kumar, Manish and Raghava, G.P.S. (2007) Support vector machine based prediction of glutathione S-transferase proteins. Protein and peptide letters, 14 (6). pp. 575-580. ISSN 0929-8665
Bhasin, Manoj and Lata, Sneh and Raghava, G.P.S. (2007) TAPPred prediction of TAP-binding peptides in antigens. Methods in molecular biology (Clifton, N.J.), 409. pp. 381-6. ISSN 1064-3745
Greenbaum, Jason A and Andersen, Pernille Haste and Blythe, Martin and Bui, Huynh-Hoa and Cachau, Raul E and Crowe, James E and Davies, Matthew and Kolaskar, A S and Lund, Ole and Morrison, Sherrie and Mumey, Brendan and Ofran, Yanay and Pellequer, Jean-Luc and Pinilla, Clemencia and Ponomarenko, Julia V and Raghava, G.P.S. and van Regenmortel, Marc H V and Roggen, Erwin L and Sette, Alessandro and Schlessinger, Avner and Sollner, Johannes and Zand, Martin and Peters, Bjoern (2007) Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. Journal of molecular recognition : JMR, 20 (2). pp. 75-82. ISSN 0952-3499
Saha, Sudipto and Zack, Jyoti and Singh, Balvinder and Raghava, G.P.S. (2006) VGIchan: prediction and classification of voltage-gated ion channels. Genomics, proteomics & bioinformatics , 4 (4). pp. 253-258. ISSN 1672-0229
Saha, Sudipto and Raghava, G.P.S. (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins, 65 (1). pp. 40-8. ISSN 1097-0134
Saha, Sudipto and Raghava, G.P.S. (2006) AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic acids research, 34 (Web Se). W202-9. ISSN 1362-4962
Kumar, Manish and Verma, Ruchi and Raghava, G.P.S. (2006) Prediction of mitochondrial proteins using support vector machine and hidden Markov model. The Journal of biological chemistry, 281 (9). pp. 5357-63. ISSN 0021-9258
Saha, Sudipto and Raghava, G.P.S. (2006) VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition. Genomics, proteomics & bioinformatics / Beijing Genomics Institute, 4 (1). pp. 42-7. ISSN 1672-0229
Singh, Mahender Kumar and Srivastava, Shilpy and Raghava, G.P.S. and Varshney, Grish C (2006) HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies. Bioinformatics (Oxford, England), 22 (2). pp. 253-5. ISSN 1367-4803
Kaundal, Rakesh and Kapoor, Amar S and Raghava, G.P.S. (2006) Machine learning techniques in disease forecasting: a case study on rice blast prediction. BMC bioinformatics, 7. p. 485. ISSN 1471-2105
Kaur, Harpreet and Raghava, G.P.S. (2006) Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network. In silico biology, 6 (1-2). pp. 111-25. ISSN 1386-6338
Kim, J.K. and Raghava, G.P.S. and Bang, S. and Choi, S. (2006) Prediction of subcellular localization of proteins using pairwise sequence alignment and support vector machin. Pattern Recognition Letters, 27. pp. 996-1001. ISSN 0167-8655
Raghava, G.P.S. and Barton, Geoffrey J (2006) Quantification of the variation in percentage identity for protein sequence alignments. BMC bioinformatics, 7. p. 415. ISSN 1471-2105
Garg, Aarti and Kaur, Harpreet and Raghava, G.P.S. (2005) Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure. Proteins, 61 (2). pp. 318-24. ISSN 1097-0134
Kumar, Manish and Bhasin, Manoj and Natt, Navjot K and Raghava, G.P.S. (2005) BhairPred: prediction of beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques. Nucleic acids research, 33 (Web Se). W154-9. ISSN 1362-4962
Bhasin, Manoj and Raghava, G.P.S. (2005) GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors. Nucleic acids research, 33 (Web Se). W143-7. ISSN 1362-4962
Bhasin, Manoj and Raghava, G.P.S. (2005) Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic acids research, 33 (Web Se). W202-7. ISSN 1362-4962
Bhasin, Manoj and Garg, Aarti and Raghava, G.P.S. (2005) PSLpred: prediction of subcellular localization of bacterial proteins. Bioinformatics (Oxford, England), 21 (10). pp. 2522-4. ISSN 1367-4803
Garg, Aarti and Bhasin, Manoj and Raghava, G.P.S. (2005) Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search. The Journal of biological chemistry, 280 (15). pp. 14427-32. ISSN 0021-9258
Saha, Sudipto and Bhasin, Manoj and Raghava, G.P.S. (2005) BCIpep: A database of B-cell epitopes. Nucleic acids research. ISSN 1362-4962
Saha, Sudipto and Bhasin, Manoj and Raghava, G.P.S. (2005) Bcipep: a database of B-cell epitopes. BMC genomics, 6. p. 79. ISSN 1471-2164
Raghava, G.P.S. and Han, Joon H (2005) Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein. BMC bioinformatics, 6. p. 59. ISSN 1471-2105
Singh, Mahender Kumar and Srivastava, Shilpy and Raghava, G.P.S. and Varshney, Grish C (2005) HaptenDB: A database of hapten molecules. Nucleic acids research. ISSN 1362-4962
Bhasin, Manoj and Raghava, G.P.S. (2005) MHCBN: A comprehensive database of MHC/TAP binders/non-binders and T-cell epitopes. Nucleic acids research. ISSN 1362-4962
Kaur, Harpreet and Raghava, G.P.S. (2004) A neural network method for prediction of beta-turn types in proteins using evolutionary information. Bioinformatics (Oxford, England), 20 (16). pp. 2751-8. ISSN 1367-4803
Issac, Biju and Raghava, G.P.S. (2004) EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches. Genome research, 14 (9). pp. 1756-66. ISSN 1088-9051
Bhasin, Manoj and Raghava, G.P.S. (2004) Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine, 22 (23-24). pp. 3195-204. ISSN 0264-410X
Bhasin, Manoj and Raghava, G.P.S. (2004) ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic acids research, 32 (Web Se). W414-9. ISSN 1362-4962
Bhasin, Manoj and Raghava, G.P.S. (2004) GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors. Nucleic acids research, 32 (Web Se). W383-9. ISSN 1362-4962
Natt, Navjot K and Kaur, Harpreet and Raghava, G.P.S. (2004) Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. Proteins, 56 (1). pp. 11-8. ISSN 1097-0134
Sharma, Deepak and Issac, Biju and Raghava, G.P.S. and Ramaswamy, R (2004) Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinformatics (Oxford, England), 20 (9). pp. 1405-12. ISSN 1367-4803
Bhasin, Manoj and Raghava, G.P.S. (2004) Classification of nuclear receptors based on amino acid composition and dipeptide composition. The Journal of biological chemistry, 279 (22). pp. 23262-6. ISSN 0021-9258
Kaur, Harpreet and Raghava, G.P.S. (2004) Role of evolutionary information in prediction of aromatic-backbone NH interactions in proteins. FEBS letters, 564 (1-2). pp. 47-57. ISSN 0014-5793
Kaur, Harpreet and Raghava, G.P.S. (2004) Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information. Proteins, 55 (1). pp. 83-90. ISSN 1097-0134
Bhasin, Manoj and Raghava, G.P.S. (2004) Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein science : a publication of the Protein Society, 13 (3). pp. 596-607. ISSN 0961-8368
Bhasin, Manoj and Raghava, G.P.S. (2004) SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence. Bioinformatics (Oxford, England), 20 (3). pp. 421-3. ISSN 1367-4803
Raghava, G.P.S. and Searle, Stephen M J and Audley, Patrick C and Barber, Jonathan D and Barton, Geoffrey J (2003) OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BMC bioinformatics, 4. p. 47. ISSN 1471-2105
Kaur, Harpreet and Raghava, G.P.S. (2003) BTEVAL: a server for evaluation of beta-turn prediction methods. Journal of bioinformatics and computational biology, 1 (3). pp. 495-504. ISSN 0219-7200
Sarin, Jyoti and Raghava, G.P.S. and Chakraborti, Pradip K (2003) Intrinsic contributions of polar amino acid residues toward thermal stability of an ABC-ATPase of mesophilic origin. Protein science : a publication of the Protein Society, 12 (9). pp. 2118-20. ISSN 0961-8368
Bhasin, Manoj and Raghava, G.P.S. (2003) Prediction of promiscuous and high-affinity mutated MHC binders. Hybridoma and hybridomics, 22 (4). pp. 229-34. ISSN 1536-8599
Singh, Harpreet and Raghava, G.P.S. (2003) ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics (Oxford, England), 19 (8). pp. 1009-14. ISSN 1367-4803
Kaur, Harpreet and Raghava, G.P.S. (2003) A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein science : a publication of the Protein Society, 12 (5). pp. 923-9. ISSN 0961-8368
Bhasin, Manoj and Singh, Harpreet and Raghava, G.P.S. (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics (Oxford, England), 19 (5). pp. 665-6. ISSN 1367-4803
Kaur, Harpreet and Raghava, G.P.S. (2003) Prediction of beta-turns in proteins from multiple alignment using neural network. Protein science : a publication of the Protein Society, 12 (3). pp. 627-34. ISSN 0961-8368
Kaur, Harpreet and Raghava, G.P.S. (2002) An evaluation of beta-turn prediction methods. Bioinformatics (Oxford, England), 18 (11). pp. 1508-14. ISSN 1367-4803
Issac, Biju and Raghava, G.P.S. (2002) GWFASTA: server for FASTA search in eukaryotic and microbial genomes. BioTechniques, 33 (3). 548-50, 552, 554. ISSN 0736-6205
Kaur, Harpreet and Raghava, G.P.S. (2002) BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms. Bioinformatics (Oxford, England), 18 (3). pp. 498-9. ISSN 1367-4803
Issac, Biju and Singh, Harpreet and Kaur, Harpreet and Raghava, G.P.S. (2002) Locating probable genes using Fourier transform approach. Bioinformatics (Oxford, England), 18 (1). pp. 196-7. ISSN 1367-4803
Singh, Harpreet and Raghava, G.P.S. (2002) Detection of Orientation of MHC Class II Binding Peptides Using Bioinformatics Tools. Biotech Software <html_ent glyph="@amp;" ascii="&"/> Internet Report, 3 (5-6). pp. 146-150. ISSN 1527-9162
Singh, H and Raghava, G.P.S. (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics (Oxford, England), 17 (12). pp. 1236-7. ISSN 1367-4803
Raghava, G.P.S. (2001) A Graphical Web Server for the Analysis of Protein Sequences and Alignment. Biotech Software <html_ent glyph="@amp;" ascii="&"/> Internet Report, 2 (6). pp. 254-257. ISSN 1527-9162
Raghava, G.P.S. (2001) PDSB: Public Domain Software in Biology. Biotech Software & Internet Report., 2 (4).
Raghava, G.P.S. (2001) PDWSB: Public Domain Web Servers in Biology. Biotech Software <html_ent glyph="@amp;" ascii="&"/> Internet Report, 2 (4). pp. 152-153. ISSN 1527-9162
Raghava, G.P.S. (2001) A Web Server for Computing the Size of DNA/Protein Fragments using a Graphical Method. Biotech Software and Internet Report, 2 (5). pp. 198-200. ISSN 1527-9162
Raghava, G.P.S. and Agrewala, J N (2001) A Web-based Method for Computing Endpoint Titer and Concentration of Antibody/Antigen. Biotech Software <html_ent glyph="@amp;" ascii="&"/> Internet Report, 2 (5). pp. 196-197. ISSN 1527-9162
Raghava, G.P.S. and Solanki, R J and Soni, V and Agrawal, Pushpa (2000) Fingerprinting method for phylogenetic classification and identification of microorganisms based on variation in 16S rRNA gene sequences. BioTechniques, 29 (1). pp. 108-116. ISSN 0736-6205
Nihalani, D and Raghava, G.P.S. and Sahni, Girish (1997) Mapping of the plasminogen binding site of streptokinase with short synthetic peptides. Protein science : a publication of the Protein Society, 6 (6). pp. 1284-92. ISSN 0961-8368
Raghava, G.P.S. (1995) DNAOPT: a computer program to aid optimization of DNA gel electrophoresis and SDS-PAGE. BioTechniques, 18 (2). 274-8, 280. ISSN 0736-6205
Raghava, G.P.S. and Goel, A and Singh, A M and Varshney, Grish C (1994) A simple microassay for computing the hemolytic potency of drugs. BioTechniques, 17 (6). pp. 1148-53. ISSN 0736-6205
Raghava, G.P.S. (1994) Improved estimation of DNA fragment length from gel electrophoresis data using a graphical method. BioTechniques, 17 (1). pp. 100-4. ISSN 0736-6205
Raghava, G.P.S. and Sahni, Girish (1994) GMAP: a multi-purpose computer program to aid synthetic gene design, cassette mutagenesis and the introduction of potential restriction sites into DNA sequences. BioTechniques, 16 (6). pp. 1116-23. ISSN 0736-6205
Raghava, G.P.S. and Agrewala, J N (1994) Method for determining the affinity of monoclonal antibody using non-competitive ELISA: a computer program. Journal of immunoassay, 15 (2). pp. 115-28. ISSN 0197-1522
Raghava, G.P.S. (1994) Recent excitement about artificial neural networks. Biobytes, 3. pp. 4-5. ISSN 0971 3271
Agrewala, J N and Raghava, G.P.S. and Mishra, G C (1993) Measurement and computation of murine interleukin-4 and interferon-gamma by exploiting the unique abilities of these lymphokines to induce the secretion of IgG1 and IgG2a. Journal of immunoassay, 14 (1-2). pp. 83-97. ISSN 0197-1522
Raghava, G.P.S. and Joshi, A and Agrewala, J N (1992) Calculation of antibody and antigen concentrations from ELISA data using a graphical method. Journal of immunological methods, 153 (1-2). pp. 263-4. ISSN 0022-1759
Saha, Sudipto and Raghava, G.P.S. (2004) BcePred: Prediction of Continuous B-cell epitopes in antigenic sequences using physico-chemical properties. In: UNSPECIFIED ICARIS 2004, 2NCS (3239). Springer Science.
Raghava, G.P.S. (1995) Computer-aided Prediction of Protein Conformation from Amino Acid Sequences of Biotechnological Relevance. PhD thesis, CSIR-IMTECH/Panjab University, Chandigarh.
