Gajendra Pal Singh RaghavaIndraprastha Institute of Information Technology | IIITD · Department of Computational Biology
Gajendra Pal Singh Raghava
M.Tech, PhD
Development of Computational Resources in the field of Biomedicine
About
613
Publications
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Introduction
Prof Raghava is a Head, Department of Computational Biology, IIIT Delhi, India. For more information see web sites
http://www.iiitd.edu.in/raghava/ and alternate web site
http://raghavagps.github.io/
Additional affiliations
March 2006 - September 2006
Education
July 1992 - July 1996
July 1984 - January 1986
July 1982 - June 1984
Publications
Publications (613)
Interferon-gamma (IFN-γ) is a versatile pleiotropic cytokine essential for both innate and adaptive immune responses. It exhibits both pro-inflammatory and anti-inflammatory properties, making it a promising therapeutic candidate for treating various infectious diseases and cancers. We present IFNepitope2, a host-specific technique to annotate IFN-...
In the past, numerous proteins/peptides have been discovered, which have a wide range of therapeutic properties like anticancer, antimicrobial, antihypertensive. Only few hundreds of proteins are druggable (approved by US FDA), most of the proteins fails in clinical trials. In this study, an attempt had been made to understand properties of FDA app...
The function of long non-coding RNA (lncRNA) is largely determined by its specific location within a cell. Previous methods have used noisy datasets, including mRNA transcripts in tools intended for lncRNAs, and excluded lncRNAs lacking significant differential localization between the cytoplasm and nucleus. In order to overcome these shortcomings,...
The stability of proteins at higher temperatures is crucial for its functionality that is measured by their melting temperature (Tm). The Tm is the temperature at which 50% of the protein loses its native structure and activity. Existing methods for predicting Tm have two major limitations: first, they are often trained on redundant proteins, and s...
Prediction of antifreeze proteins (AFPs) holds significant importance due to their diverse applications in healthcare. An inherent limitation of current AFP prediction methods is their reliance on unreviewed proteins for evaluation. This study evaluates, proposed and existing methods on an independent dataset containing 80 AFPs and 73 non‐AFPs obta...
Transcription factors are essential DNA-binding proteins that regulate the transcription rate of several genes and control the expression of genes inside a cell. The prediction of transcription factors with high precision is important for understanding biological processes such as cell differentiation, intracellular signaling, and cell-cycle contro...
Several peptide-based drugs fail in clinical trials due to their toxicity or hemolytic activity against red blood cells (RBCs). Existing methods predict hemolytic peptides but not the concentration (HC50) required to lyse 50% of RBCs. In this study, we developed a classification model and regression model to identify and quantify the hemolytic acti...
Plant Disease Resistance (PDR) proteins are critical in identifying and killing plant pathogens. Predicting PDR protein is essential for understanding plant-pathogen interactions and developing strategies for crop protection. This study proposes a hybrid model for predicting and designing PDR proteins against plant-invading pathogens. Initially, we...
In the past, several methods have been developed for predicting antibacterial and antimicrobial peptides, but only limited attempts have been made to predict their minimum inhibitory concentration (MIC) values. In this study, we trained our models on 3,143 peptides and validated them on 786 peptides whose MIC values have been determined experimenta...
In this study, we investigated the properties of exosomal miRNAs to identify potential biomarkers for liquid biopsy. We collected 956 exosomal and 956 non-exosomal miRNA sequences from RNALocate and miRBase to develop predictive models. Our initial analysis reveals that specific nucleotides are preferred at certain positions in miRNAs associated wi...
Long non-coding RNAs (lncRNAs) play a vital role in biological processes, and their dysfunctions lead to a wide range of diseases. Due to advancements in sequencing technology, more than 20,000 lncRNA transcripts have been identified in humans, almost equivalent to coding transcripts. One crucial aspect in annotating lncRNA function is predicting t...
Prediction of antifreeze proteins (AFPs) holds significant importance due to their diverse applications in healthcare. An inherent limitation of current AFP prediction methods is their reliance on unreviewed proteins for evaluation. This study evaluates proposed and existing methods on an independent dataset containing 81 AFPs and 73 non-AFPs obtai...
Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture...
Most of the existing methods developed for predicting antibacterial peptides (ABPs) are mostly designed to target either gram-positive or gram-negative bacteria. In this study, we describe a method that allows us to predict ABPs against gram-positive, gram-negative, and gram-variable bacteria. Firstly, we developed an alignment-based approach using...
In the past, several methods have been developed for predicting the single-label subcellular localization of messenger RNA (mRNA). However, only limited methods are designed to predict the multi-label subcellular localization of mRNA. Furthermore, the existing methods are slow and cannot be implemented at a transcriptome scale. In this study, a fas...
Background
HLA-DRB1*04:01 is associated with many diseases including sclerosis, arthritis, diabetes, and Covid19. Thus, it is important to scan binders of HLA-DRB1*04:01 in an antigen to develop immunotherapy, vaccines, and protection against these diseases. One of the major limitations of existing methods for predicting with HLA-DRB1*04:01 binders...
The identification of B‐cell epitopes (BCEs) in antigens is a crucial step in developing recombinant vaccines or immunotherapies for various diseases. Over the past four decades, numerous in silico methods have been developed for predicting BCEs. However, existing reviews have only covered specific aspects, such as the progress in predicting confor...
Computational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDS TB )....
Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most highly prevalent cancer type worldwide. Early detection of HNSCC is one of the important challenges in managing the treatment of the cancer patients. Existing techniques for detecting HNSCC are costly, expensive, and invasive in nature. In this study, we aimed to address this issue b...
Toxicity emerges as a prominent challenge in the design of therapeutic peptides, causing the failure of numerous peptides during clinical trials. In 2013, our group developed ToxinPred, a computational method that has been extensively adopted by the scientific community for predicting peptide toxicity. In this paper, we propose a refined variant of...
Non-invasive diagnostics and therapies are crucial to prevent patients from undergoing painful procedures. Exosomal proteins can serve as important biomarkers for such advancements. In this study, we attempted to build a model to predict exosomal proteins. All models are trained, tested, and evaluated on a non-redundant dataset comprising 2831 exos...
HLA-DRB1*04:01 is associated with many disease that include sclerosis, arthritis, diabetes and Covid19. Thus, it is important to scan binders of HLA-DRB1*04:01 in an antigen to develop immunotherapy, vaccine and protection against these diseases. One of the major limitations of existing methods for predicting with HLA-DRB1*04:01 binders is that the...
This study focuses on the development of in silico models for predicting antibacterial peptides as a potential solution for combating antibiotic-resistant strains of bacteria. Existing methods for predicting antibacterial peptides are mostly designed to target either gram-positive or gram-negative bacteria. In this study, we introduce a novel appro...
Alzheimer's disease (AD) is a progressive neurological disorder characterized by brain cell death, brain atrophy, and cognitive decline. Early diagnosis of AD remains a significant challenge in effectively managing this debilitating disease. In this study, we aimed to harness the potential of single-cell transcriptomics data from 12 Alzheimer's pat...
Purpose: Hormones play a critical role in regulating various physiological processes and any hormonal imbalances can lead to major endocrine disorders. Thus, studying hormones is essential for both the therapeutics and the diagnostics of hormonal diseases. To facilitate this need, we have developed Hmrbase2, a comprehensive platform that provides e...
Interleukin 6 (IL6) is a major pro-inflammatory cytokine that plays a pivotal role in both innate and adaptive immune responses. In the past, a number of studies reported that high level of IL6 promotes the proliferation of cancer, autoimmune disorders, and cytokine storm in COVID-19 patients. Thus, it is extremely important to identify and remove...
Interleukins are a distinctive class of molecules exhibiting various immune signaling functions. Immunoregulatory cytokine, Interleukin 13 (IL13), is primarily synthesized by activated T-helper 2 cells, mast cells, and basophils. IL13, is known to stimulate many allergic and autoimmune diseases, such as asthma, rheumatoid arthritis, systemic sclero...
Peptide hormones are genome-encoded signal transduction molecules released in multicellular organisms. The dysregulation of hormone release can cause multiple health problems and it is crucial to study these hormones for therapeutic purposes. To help the research community working in this field, we developed a prediction server that classifies horm...
Interleukin-5 (IL-5) can act as an enticing therapeutic target due to its pivotal role in several eosinophil-mediated diseases. The aim of this study is to develop a model for predicting IL-5 inducing antigenic regions in a protein with high precision. All models in this study have been trained, tested and validated on experimentally validated 1907...
Tumor Necrosis Factor alpha (TNF-α) is a pleiotropic pro-inflammatory cytokine that is crucial in controlling the signaling pathways within the immune cells. Recent studies reported that higher expression levels of TNF-α are associated with the progression of several diseases, including cancers, cytokine release syndrome in COVID-19, and autoimmune...
Phage therapy is a viable alternative to antibiotics for treating microbial infections, particularly managing drug-resistant strains of bacteria. One of the major challenges in designing phage-based therapy is to identify the most appropriate potential phage candidate to treat bacterial infections. In this study, an attempt has been made to predict...
Saliva as a non-invasive diagnostic fluid has immense potential as a tool for early diagnosis and prognosis of patients. The information about salivary biomarkers is broadly scattered across various resources and research papers. It is important to bring together all the information on salivary biomarkers to a single platform. This will accelerate...
Saliva as a non-invasive diagnostic fluid has immense potential as a tool for early diagnosis and prognosis of patients. The information about salivary biomarkers is broadly scattered across various resources and research papers. It is important to bring together all the information on salivary biomarkers to a single platform. This will accelerate...
Background and objective
Hormones are essential for cell communication and hence regulate various physiological processes. The discrepancies in the hormones or their receptors can break this communication and cause major endocrinological disorders. It is, therefore, indispensable for the therapeutics and diagnostics of hormonal diseases.
Methods
W...
Identification of secretory proteins in body fluids is one of the key challenges in the development of non-invasive diagnostics. It has been shown in the part that a significant number of proteins are secreted by cells via exosomes called exosomal proteins. In this study, an attempt has been made to build a model that can predict exosomal proteins...
A host-specific technique has been developed for annotating interferon-gamma (IFN-γ) inducing peptides, it is an updated version of IFNepitope. In this study, dataset used for developing prediction method contain experimentally validated 25492 and 7983 IFN-γ inducing peptides in human and mouse host, respectively. In initial phase, machine learning...
Over the years, numerous vaccines have been developed against viral infections; however, a complete database that provides comprehensive information on viral vaccines has been lacking. In this review, along with our freely accessible database ViralVacDB, we provide details of the viral vaccines, their type, routes of administration and approving ag...
B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitopes in an antigen. In this study, a single method was developed for predicting both types (linear/conformational...
Introduction
Celiac disease (CD) is an autoimmune gastrointestinal disorder causes immune-mediated enteropathy against gluten. Gluten immunogenic peptides have the potential to trigger immune responses which leads to damage the small intestine. HLA-DQ2/DQ8 are major alleles that bind to epitope/antigenic region of gluten and induce celiac disease....
In the past, number of methods have been developed for predicting single label subcellular localization of mRNA in a cell. Only limited methods had been built to predict multi-label subcellular localization of mRNA. Most of the existing methods are slow and cannot be implemented at transcriptome scale. In this study, a fast and reliable method had...
In the current era, one of the major challenges is to manage the treatment of drug/antibiotic-resistant strains of bacteria. Phage therapy, a century-old technique, may serve as an alternative to antibiotics in treating bacterial infections caused by drug-resistant strains of bacteria. In this review, a systematic attempt has been made to summarize...
There are a number of antigens that induce autoimmune response against β-cells, leading to type 1 diabetes mellitus (T1DM). Recently, several antigen-specific immunotherapies have been developed to treat T1DM. Thus, identification of T1DM associated peptides with antigenic regions or epitopes is important for peptide based-therapeutics (e.g. immuno...
This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and independent/validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the vali...
Influenza A is a contagious viral disease responsible for four pandemics in the past and a major public health concern. Being zoonotic in nature, the virus can cross the species barrier and transmit from wild aquatic bird reservoirs to humans via intermediate hosts. In this study, we have developed a computational method for the prediction of human...
Sigma70 factor plays a crucial role in prokaryotes and regulates the transcription of most of the housekeeping genes. One of the major challenges is to predict the sigma70 promoter or sigma70 factor binding site with high precision. In this study, we trained and evaluate our models on a dataset consists of 741 sigma70 promoters and 1,400 non-promot...
Interleukin-5 (IL-5) is the key cytokine produced by T-helper, eosinophils, mast and basophils cells. It can act as an enticing therapeutic target due to its pivotal role in several eosinophil-mediated diseases. Though numerous methods have been developed to predict HLA binders and cytokines-inducing peptides, no method was developed for predicting...
Advancements in cancer immunotherapy have shown significant outcomes in treating various types of cancers. In order to design effective immunotherapy, it is important to understand immune response of a patient based on its genomic profile. We compute prognostic biomarkers from 8346 cancer patients for twenty types of cancer. These prognostic biomar...
In the last three decades, a wide range of protein features have been discovered to annotate a protein. Numerous attempts have been made to integrate these features in a software package/platform so that the user may compute a wide range of features from a single source. To complement the existing methods, we developed a method, Pfeature, for compu...
Background
Bacterial diseases are one of the leading causes of millions of fatalities worldwide, mainly due to antimicrobial resistance. The discovery of chicken cholera vaccine in 1879 revolutionized our fight against bacterial infections. Bacterial vaccines are proven to be highly effective in preventing many infectious diseases. Currently, vario...
DNA–protein interaction is one of the most crucial interactions in the biological system, which decides the fate of many processes such as transcription, regulation and splicing of genes. In this study, we trained our models on a training dataset of 646 DNA-binding proteins having 15 636 DNA interacting and 298 503 non-interacting residues. Our tra...
Tumor Necrosis Factor alpha (TNF-α) is a pleiotropic pro-inflammatory cytokine that plays a crucial role in controlling signaling pathways within the immune cells. Recent studies reported that the higher expression levels of TNF-α is associated with the progression of several diseases including cancers, cytokine release syndrome in COVID-19 and aut...
Celiac disease (CD) is an autoimmune gastrointestinal disorder which causes immune-mediated enteropathy against gluten. The gluten immunogenic peptides have the potential to trigger immune responses which leads to damage the small intestine. HLA-DQ2 and HLA-DQ8 are major alleles that bind to epitope/antigenic region of gluten and induce celiac dise...
There are a number of antigens that induce autoimmune response against β-cells, leading to Type 1 diabetes mellitus (T1DM). Recently several antigen-specific immunotherapies have been developed to treat T1DM. Thus identification of T1DM associated peptides with antigenic regions or epitopes is important for peptide based-therapeutics (e.g., immunot...
Transcription factors (TFs) are essential DNA-binding proteins that regulate the rate of transcription of several genes and controls the expression of genes inside a cell. The prediction of TFs with high precision is important for understanding number of biological processes such as cell-differentiation, intracellular signaling, cell-cycle control....
Parkinson's disease (PD) is the second most common neurodegenerative disease. The presence of lewy bodies, primarily consisting of α-synuclein (α-syn) aggregates is one of the common features seen in the substantia nigra region of the brain in PD patients. The disease remains incurable and only symptomatic relief is available. We screened various c...
This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the validation datas...
Phage therapy is a viable alternative to antibiotics for treating microbial infections, particularly managing drug-resistant strains of bacteria. One of the major challenges in designing phage based therapy is to identify the most appropriate phage to treat a bacterial infection. In this study, an attempt has been made to predict phage-host interac...
Identification of somatic mutations with high precision is one of the major challenges in the prediction of high-risk liver-cancer patients. In the past, number of mutations calling techniques have been developed that include MuTect2, MuSE, Varscan2, and SomaticSniper. In this study, an attempt has been made to benchmark the potential of these tech...
Proteins/peptides have shown to be promising therapeutic agents for a variety of diseases. However, toxicity is one of the obstacles in protein/peptide-based therapy. The current study describes a web-based tool, ToxinPred2, developed for predicting the toxicity of proteins. This is an update of ToxinPred developed mainly for predicting toxicity of...
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional HLA-based immunotherapy, particularly against cancer and COVID-19 infection. In the last two decades...
Influenza A is a contagious viral disease responsible for four pandemics in the past and a major public health concern. Being zoonotic in nature, the virus can cross the species barrier and transmit from wild aquatic bird reservoirs to humans via intermediate hosts. Virus gradually undergoes host adaptive mutations in their genome and proteins, res...
Background
Interleukin 13 (IL-13) is an immunoregulatory cytokine, primarily released by activated T-helper 2 cells. IL-13 induces the pathogenesis of many allergic diseases, such as airway hyperresponsiveness, glycoprotein hypersecretion, and goblet cell hyperplasia. In addition, IL-13 inhibits tumor immunosurveillance, leading to carcinogenesis....
Immunotherapy is a rapidly growing therapy for cancer which have numerous benefits over conventional treatments like surgery, chemotherapy, and radiation. Overall survival of cancer patients has improved significantly due to the use of immunotherapy. It acts as a novel pillar for treating different malignancies from their primary to the metastatic...
In the past few decades, a large number of cell-penetrating peptides (CPPs) have been discovered. These CPPs have a wide range of applications including drug delivery vehicles. Numerous in silico tools have been developed over the years to design and predict the cell-penetrating peptides that contain natural amino acids. The majority of natural cel...
Purpose
Identification of somatic mutations with high precision is one of the major challenges in prediction of high-risk liver-cancer patients. In the past number of mutation calling techniques have been developed that include MuTect2, MuSE, Varscan2, and SomaticSniper. In this study an attempt has been made to benchmark potential of these techniq...