Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of

Open Source for Drug Discovery Open Source Drug Discovery is a Council of Scientific and Industrial Research, India (CSIR)-led Team India Consortium with global participation offering a collaborative drug discovery platform for neglected tropical diseases like leishmaniasis, whi ...

(OSDD). The CRDD web portal provides computer resources related to

drug discovery In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered. Historically, drugs were discovered by identifying the active ingredient from traditional remedies or by ...

on a single platform. It provides computational resources for researchers in computer-aided

drug design Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that acti ...

, a discussion forum, and resources to maintain

Wikipedia Wikipedia is a multilingual free online encyclopedia written and maintained by a community of volunteers, known as Wikipedians, through open collaboration and using a wiki-based editing system. Wikipedia is the largest and most-read refer ...

related to drug discovery, predict inhibitors, and predict the

ADME-Tox ADME is an abbreviation in pharmacokinetics and pharmacology for " absorption, distribution, metabolism, and excretion", and describes the disposition of a pharmaceutical compound within an organism. The four criteria all influence the drug l ...

property of molecules One of the major objectives of CRDD is to promote open source

software Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

in the field of

chemoinformatics Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive proble ...

and pharmacoinformatics.

Features

Under CRDD, all the resources related to computer-aided drug design have been collected and compiled. These resources are organized and presented on CRDD so users can get resources from a single source. *Target identification provides the resources important for searching drug targets with information on

genome annotation DNA annotation or genome annotation is the process of identifying the locations of genes and all of the coding regions in a genome and determining what those genes do. An annotation (irrespective of the context) is a note added by way of explanati ...

, proteome annotation, potential targets, and

protein structure Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer ma ...

*Virtual screening compiles the resources important for virtual screening as QSAR techniques, docking QSAR, chemoinformatics, and

siRNA Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating wi ...

miRNA MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRN ...

*Drug design provides the resources important for designing drug inhibitors/molecules as lead optimization, pharmacoinformatics, ADMET, and clinical informatics

Community contribution

Under this category platform has been developed where the community may contribute in the process of drug discovery. *DrugPedia: A Wikipedia for Drug Discovery is a Wiki created for collecting and compiling information related to computer-aided drug design. It is developed under the umbrella of Open Source Drug Discovery (OSDD) project and covers a wide range of subjects around drugs like

Bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

, Cheminformatics, clinical informatics etc. *Indipedia: A Wikipedia for

India India, officially the Republic of India (Hindi: ), is a country in South Asia. It is the seventh-largest country by area, the second-most populous country, and the most populous democracy in the world. Bounded by the Indian Ocean on the so ...

is a Wiki for collecting and compiling drug information related to India. It is intended is to provide comprehensive information about India created for Indians by Indians. It is developed under the umbrella of Open Source Drug Discovery (OSDD) project. *The CRDD Forum was launched to discuss the challenge in developing computational resources for drug discovery.

Indigenous development: software and web services

Beside collecting and compiling resources, CRDD members develop new software and web services. All services developed are free for academic use. The following are a few major tools developed at CRDD.

Development of databases

*HMRBase: It is a manually curated

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...

Hormones A hormone (from the Ancient Greek, Greek participle , "setting in motion") is a class of cell signaling, signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and beh ...

and their

Receptors Receptor may refer to: *Sensory receptor, in physiology, any structure which, on receiving environmental stimuli, produces an informative nerve impulse *Receptor (biochemistry), in biochemistry, a protein molecule that receives and responds to a n ...

. It is a compilation of sequence data after extensive manual literature search and from publicly available databases. Hombres can be searched on the basis of a variety of data types. Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hombres are hormone-receptor pair-related information, mapping of peptide stretches on the

protein sequences Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...

of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission. This database integrated in drug media so public can contribute. *BIAdb: A Database for

Benzylisoquinoline Substitution of the heterocycle isoquinoline at the C1 position by a benzyl group provides 1‑benzylisoquinoline, the most widely examined of the numerous benzylisoquinoline structural isomers. The 1-benzylisoquinoline moiety can be identified wi ...

Alkaloids Alkaloids are a class of basic, naturally occurring organic compounds that contain at least one nitrogen atom. This group also includes some related compounds with neutral and even weakly acidic properties. Some synthetic compounds of similar st ...

. The Benzylisoquinoline Alkaloid Database is an attempt to gather the scattered information related to the BIA's. Many BIA's show therapeutic properties and can be considered as potent drug candidates. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database integrated in drugpedia so public can contribute. *Antigen DB: This database contain more than 500

antigens In immunology, an antigen (Ag) is a molecule or molecular structure or any foreign particulate matter or a pollen grain that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response. ...

collected from literature and other immunological resources. These antigens come from 44 important pathogenic species. In Antigen DB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and

T-cell A T cell is a type of lymphocyte. T cells are one of the important white blood cells of the immune system and play a central role in the adaptive immune response. T cells can be distinguished from other lymphocytes by the presence of a T-cell rec ...

epitopes An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The epitope is the specific piece of the antigen to which an antibody binds. The p ...

, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases. *PolysacDB: The PolysacDB is dedicated to provide comprehensive information about antigenic

polysaccharides Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with w ...

of microbial origin (

bacterial Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

and

fungal A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from th ...

antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

against them, proposed epitopes, structural detail, proposed functions, assay system, cross-reactivity related information and much more. It is a manually curated database where most of data has been collected from

PubMed PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the ...

and

PubMed Central PubMed Central (PMC) is a free digital repository that archives open access full-text scholarly articles that have been published in biomedical and life sciences journals. As one of the major research databases developed by the National Center f ...

literature databases. *TumorHope: TumorHope is a manually curated comprehensive database of experimentally characterized

tumor A neoplasm () is a type of abnormal and excessive growth of tissue. The process that occurs to form or produce a neoplasm is called neoplasia. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and persists ...

homing peptides. These peptides recogninze tumor tissues and tumor associated micro environment, including tumor

metastasis Metastasis is a pathogenic agent's spread from an initial or primary site to a different or secondary site within the host's body; the term is typically used when referring to metastasis by a cancerous tumor. The newly pathological sites, then, ...

. *ccPDB: The ccPDB database is designed to provide service to scientific community working in the field of function or structure annotation of proteins. This database of datasets is based on

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...

(PDB), where all datasets were derived from PDB. *OSDDchem: OSDDChem chemical database is an open repository of information on synthesised, semi-synthesized, natural and virtually designed molecules from the OSDD community. *CancerDR: CancerDR is a database of 148

anticancer drugs Chemotherapy (often abbreviated to chemo and sometimes CTX or CTx) is a type of cancer treatment that uses one or more anti-cancer drugs (chemotherapeutic agents or alkylating agents) as part of a standardized chemotherapy regimen. Chemotherap ...

and their effectiveness against around 1000 cancer cell lines. These are target based drugs, CancerDR maintain comprehensive information about these drugs their target

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

/protein and

cell lines An immortalised cell line is a population of cells from a multicellular organism which would normally not proliferate indefinitely but, due to mutation, have evaded normal cellular senescence and instead can keep undergoing division. The cells ...

Software developed

*MycoTB: In order to assist scientific community, we extended flexible system concept for building standalone software MycoTB for

Windows Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

Users. MycoTB is one of the computer program developed under OSDD/CRDD programme. This software allow user to build their own flexible system on their personal computers to manage and annotate whole proteome of MycoTB.

Resources created

*CRAG: Computational resources for assembling genomes (CRAG) has been to assist the users in assembling of genomes from short read sequencing (SRS). Following major objective; i) Collection and compilation of computation resources, ii) Brief description of genome assemblers, iii) Maintaining SRS and related data, iv) Service to community to assemble their genomes *CRIP: Computational resources for predicting protein–macromolecular interactions (CRIP) developed to provide resources related interaction. This site maintain large number of resources on interaction world of proteins that includes, protein–protein, protein– DNA, protein–ligand, protein–

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

. *BioTherapy: Bioinformatics for Therapeutic Peptides and Proteins (BioTherapi) developed for researchers working in the field of protein/peptide therapeutics. At present there is no single platform that provide this kind of information. This site include all the relevant information about the use of Peptides/Proteins in drug and synthesis of new peptides. It also cover problems, in their formulation, synthesis and delivery process *HiveBio: HIV Bioinformatics (HIVbio) site contains various types of information on

Human Immunodeficiency Virus The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause AIDS, acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the ...

(HIV) life cycle and Infection. *GDP bio: GDP bio (Genome based prediction of Diseases and Personal medicines using Bioinformatics) is the project focussed upon providing various resources related to genome analysis particularly for the prediction of disease susceptibility of a particular individual and personalized medicines development, aiming public health improvement. *AminoFAST: Functional Annotation Tools for Amino Acids (AminoFAST) server is designed to serve the bioinformatics community. Aim is to develop as many as possible tools to understand function of amino acids in proteins based on protein structure in PDB. The broad knowledge of proteins function would help in the identification of noval drug targets.

Web services for chemoinformatics

First time in the world CRDD team has developed open source platform which allows users to predict inhibitors against novel M.

Tuberculosis Tuberculosis (TB) is an infectious disease usually caused by '' Mycobacterium tuberculosis'' (MTB) bacteria. Tuberculosis generally affects the lungs, but it can also affect other parts of the body. Most infections show no symptoms, in ...

drug targets and other important properties of drug molecules like ADMET. Following are list of few servers. *MetaPred: A webserver for the Prediction of

Cytochrome P450 Cytochromes P450 (CYPs) are a Protein superfamily, superfamily of enzymes containing heme as a cofactor (biochemistry), cofactor that functions as monooxygenases. In mammals, these proteins oxidize steroids, fatty acids, and xenobiotics, and are ...

Isoform responsible for Metabolizing a Drug Molecule. MetaPred Server predict metabolizing CYP isoform of a drug molecule/substrate, based on SVM models developed using CDK descriptors. This server will be helpful for researcher working in the field of drug discovery. This study demonstrates that it is possible to develop free web servers in the field of chemoinformatics. This will encourage other researchers to develop web server for public use, which may lead to decrease the cost of discovering new drug molecules. *ToxiPred: A server for prediction of aqueous toxicity of small chemical molecules in T. pyriformis. *KetoDrug:A web server for binding affinity prediction of ketoxazole derivatives against

Fatty Acid Amide Hydrolase Fatty acid amide hydrolase or FAAH (, oleamide hydrolase, anandamide amidohydrolase) is a member of the serine hydrolase family of enzymes. It was first shown to break down anandamide in 1993. In humans, it is encoded by the gene ''FAAH''.; Fun ...

(FAAH). It is a user friendly web server for the prediction of binding affinity of small chemical molecules against FAAH. *KiDoQ: KiDoQ, a web server has been developed to serve scientific community working in the field of designing inhibitors against

Dihydrodipicolinate synthase 4-Hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7, dihydrodipicolinate synthase, dihydropicolinate synthetase, dihydrodipicolinic acid synthase, L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing), ''dapA (gene)'') is an enz ...

(DHDPS), a potential drug target enzyme of a unique bacterial DAP/Lysine pathway. *GDoQ: GDoQ (Prediction of GLMU inhibitors using QSAR and

AutoDock AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the re ...

) is an open source platform developed for predicting inhibitors against ''

Mycobacterium tuberculosis ''Mycobacterium tuberculosis'' (M. tb) is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis. First discovered in 1882 by Robert Koch, ''M. tuberculosis'' has an unusual, waxy coating on its c ...

'' (M.Tb) drug target N-acetylglucosamine-1-phosphate uridyltransferase (GLMU) protein. This is a potential drug target involved in bacterial cell wall synthesis. This server uses molecular docking and QSAR strategies to predict inhibitory activity value (IC50) of chemical compounds for GLMU protein. *ROCR: The ROCR is an R package for evaluating and visualizing classifier performance . It is a flexible tool for creating ROC graphs, sensitivity/specificity curves, area under curve and precision/recall curve. The parametrization can be visualized by coloring the curve according to cutoff. *WebCDK: A web interface for CDK library, it is a web interface for predicting descriptors of chemicals using CDK library. *Pharmacokinetics: The Pharmacokinetic data analysis determines the relationship between the dosing regimen and the body's exposure to the drug as measured by the nonlinear concentration time curve. It includes a function, AUC, to calculate area under the curve. It also includes functions for half-life estimation for a biexponential model, and a two phase linear regression

Prediction and analysis of drug targets

*RNApred: Prediction of RNAbinding proteins from ints amino acid sequence. *ProPrint: Prediction of interaction between proteins from their amino acid sequence. *DomPrint: Domprint is a domain-domain interaction (DDI) prediction server. *MycoPrint: MycoPrint is a web interface for exploration of the interactome of ''Mycobacterium tuberculosis ''H37Rv (Mtb) predicted by "Domain Interaction Mapping" (DIM) method. *ATPint: A server for predicting ATP interacting residues in proteins. *FADpred: Identification of

FAD A fad or trend is any form of collective behavior that develops within a culture, a generation or social group in which a group of people enthusiastically follow an impulse for a short period. Fads are objects or behaviors that achieve short- ...

interacting residues in proteins. *GTPbinder: Prediction of protein GTP interacting residues. *NADbinder: Prediction of NAD binding residues in proteins. *PreMier: Designing of Mutants of Antibacterial Peptides. *DMAP: DMAP: Designing of Mutants of Antibacterial Peptides *icaars:Prediction and classification of

aminoacyl tRNA synthetase An aminoacyl-tRNA synthetase (aaRS or ARS), also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. It does so by catalyzing the transesterification of a specific cognate amino acid or its pre ...

s using PROSITE domains *CBtope: Prediction of Conformational B-cell epitope in a sequence from its amino acid sequence. *DesiRM: Designing of Complementary and Mismatch siRNAs for Silencing a Gene . *GenomeABC: A server for Benchmarking of Genome Assemblers.