/// <summary> /// Author: Andy Tang /// </summary> public static PDB_Information GetPDBInfo(Protein_Information protein, Drug_Information drug) { PDB_Information PDBInfo = null; if (protein == null || drug == null) { return(PDBInfo); } string uniprot_ID = protein.Uniprot_ID; string drug_PDB_ID = drug.Drug_PDB_ID; using (DrugProNETEntities context = new DrugProNETEntities()) { DbSet <PDB_Information> dbSet = context.PDB_Information; foreach (PDB_Information pdb in dbSet) { if (string.Equals(pdb.Uniprot_ID, uniprot_ID, StringComparison.OrdinalIgnoreCase) && string.Equals(pdb.Drug_PDB_ID, drug_PDB_ID, StringComparison.OrdinalIgnoreCase)) { PDBInfo = pdb; } } } return(PDBInfo); }
/// <summary> /// Author: Andy Tang /// </summary> protected void Search_Textbox_Changed(object sender, EventArgs e) { search_drop_down.Items.Clear(); search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); List <Protein_Information> proteinList = new List <Protein_Information>(); const int minPrefixLength = 3; if (search_textBox.Text.Length < minPrefixLength) { return; } Drug_Information drug = EF_Data.GetDrugsQuery(search_textBox.Text).FirstOrDefault(); if (drug != null) { List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingDrug(drug.Drug_PDB_ID); foreach (PDB_Information pdb in pdbInfoList) { Protein_Information protein = EF_Data.GetProteinByUniprotID(pdb.UniProt_ID); if (protein != null) { proteinList.Add(protein); } } } if (proteinList.Count > 0) { List <string> valuesList = new List <string>(); foreach (Protein_Information protein in proteinList) { valuesList.Add(protein.UniProt_ID); valuesList.Add(protein.Protein_Short_Name); valuesList.Add(protein.Protein_Full_Name); valuesList.Add(protein.Protein_Alias); valuesList.Add(protein.NCBI_RefSeq_NP_ID); valuesList.Add(protein.PhosphoNET_Name); valuesList.Add(protein.PDB_Protein_Name); } valuesList = DataUtilities.FilterDropdownList(valuesList); foreach (string value in valuesList) { search_drop_down.Items.Add(new ListItem(value, value, true)); } } else { search_drop_down.Items.Clear(); search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE); } }
/// <summary> /// Author: Andy Tang /// </summary> protected void Search_Textbox_Changed(object sender, EventArgs e) { search_drop_down.Items.Clear(); search_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); List <Drug_Information> drugList = new List <Drug_Information>(); const int minPrefixLength = 3; if (search_textBox.Text.Length < minPrefixLength) { return; } Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault(); if (protein != null) { List <PDB_Information> pdbInfoList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID); foreach (PDB_Information pdb in pdbInfoList) { Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID); if (drug != null) { drugList.Add(drug); } } } if (drugList.Count > 0) { List <string> valuesList = new List <string>(); foreach (Drug_Information drug in drugList) { valuesList.Add(drug.Other_Drug_Name_Alias); valuesList.Add(drug.Drug_Common_Name); valuesList.Add(drug.Drug_Chemical_Name); valuesList.Add(drug.Compound_CAS_ID); valuesList.Add(drug.PubChem_CID); valuesList.Add(drug.ChEMBL_ID); } valuesList = DataUtilities.FilterDropdownList(valuesList); foreach (string value in valuesList) { search_drop_down.Items.Add(new ListItem(value, value, true)); } } else { search_drop_down.Items.Clear(); search_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE); } }
/// <summary> /// Author: Ryan Liang /// </summary> public void LoadDrug(Drug_Information drug, SNV_Mutation mutation) { ProcessRow(PDB_drug_ID_row, PDB_drug_ID, mutation.Drug_PDB_ID, drug.Drug_PDB_ID_URL); ProcessRow(drug_name_row, drug_name, drug.Drug_Common_Name); ProcessRow(pubchem_cid_row, pubchem_cid, drug.PubChem_CID, drug.PubChem_Compound_Link); ProcessRow(chembl_id_row, chembl_id, drug.ChEMBL_ID, drug.ChEMBL_Link); ProcessRow(chemspider_id_row, chemspider_id, drug.ChemSpider_ID, drug.ChemSpider_Link); ProcessRow(drugbank_id_row, drugbank_id, drug.DrugBank_ID, drug.DrugBank_Link); ProcessRow(drug_information_result_url_row, drug_information_result_url, "Click here for more drug information from DrugProNET", "DrugInfoResult.aspx?query_string=" + drug.Drug_Name_for_Pull_Down_Menu); }
protected void Search_Textbox_Changed(object sender, EventArgs e) { drug_specification_drop_down.Items.Clear(); drug_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); amino_acid_specification_drop_down.Items.Clear(); amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); const int minPrefixLength = 3; if (search_textBox.Text.Length < minPrefixLength) { return; } Protein_Information protein = EF_Data.GetProteinsInfoQuery(search_textBox.Text).FirstOrDefault(); if (protein != null) { List <PDB_Information> pdbList = EF_Data.GetPDBInfoUsingProtein(protein.UniProt_ID); List <Drug_Information> drugList = new List <Drug_Information>(); foreach (PDB_Information pdb in pdbList) { Drug_Information drug = EF_Data.GetDrugByDrugPDBID(pdb.Drug_PDB_ID); if (drug != null) { drugList.Add(drug); } } if (drugList.Count > 0) { List <string> dropdownValues = new List <string>(); foreach (Drug_Information drug in drugList) { dropdownValues.Add(drug.Drug_Name_for_Pull_Down_Menu); } dropdownValues = DataUtilities.FilterDropdownList(dropdownValues); foreach (string dropdownValue in dropdownValues) { drug_specification_drop_down.Items.Add(dropdownValue); } } else { drug_specification_drop_down.Items.Clear(); drug_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE); } } }
/// <summary> /// Author: Ryan Liang /// </summary> public static Drug_Information GetDrugByDrugPDBID(string query) { Drug_Information drug = null; using (DrugProNETEntities context = new DrugProNETEntities()) { drug = context.Drug_Information.Where(d => d.Drug_PDB_ID.ToLower().Contains(query.ToLower())).FirstOrDefault(); } return(drug); }
/// <summary> /// Author: Ryan Liang /// </summary> public static Drug_Information GetDrugUsingDropDownName(string query) { Drug_Information drug = null; using (DrugProNETEntities context = new DrugProNETEntities()) { drug = context.Drug_Information.Where(d => d.Drug_Name_for_Pull_Down_Menu.ToLower().Contains(query.ToLower())).FirstOrDefault(); } return(drug); }
/// <summary> /// Author: Ryan Liang /// </summary> private TableRow CreateTableRow(Drug_Information drug, PDB_Interaction interaction, SNV_Mutation mutation) { TableRow tableRow = new TableRow(); tableRow.Cells.Add(new TableCell() { Text = drug.Drug_Common_Name }); tableRow.Cells.Add(new TableCell() { Text = mutation.PDB_File_ID }); tableRow.Cells.Add(new TableCell() { Text = mutation.Drug_PDB_ID }); tableRow.Cells.Add(new TableCell() { Text = drug.PubChem_CID }); tableRow.Cells.Add(new TableCell() { Text = drug.ChEMBL_ID }); if (double.TryParse(interaction?.Interaction_Distance_Ratio, out double result)) { tableRow.Cells.Add(new TableCell() { Text = result.ToString("0.0") }); } else { tableRow.Cells.Add(new TableCell() { Text = "" }); } string predictedEffiency = FindPredictedEffiency(mutation); tableRow.Cells.Add(new TableCell() { Text = predictedEffiency }); return(tableRow); }
/// <summary> /// Author: Ryan Liang /// </summary> public void LoadDrug(Drug_Information drug, PDB_Information PDB_Info) { ProcessRow(PDB_drug_ID_row, PDB_drug_ID, drug.Drug_PDB_ID); ProcessRow(drug_name_row, drug_name, drug.Drug_Common_Name); ProcessRow(drug_chemical_name, drug_chemical_name, drug.Drug_Chemical_Name); ProcessRow(drug_alias_row, drug_alias, drug.Other_Drug_Name_Alias); ProcessRow(drug_formula_row, drug_formula, drug.Drug_Formula); ProcessRow(drug_mass_da_row, drug_mass_da, drug.Molecular_Mass); ProcessRow(potency_row, potency, "IC50 (nM):" + PDB_Info.IC50_nM_ + " (BINDINGDB); Ki (nM): " + PDB_Info.Ki_nM_ + " (BINDINGDB); Kd(nM): " + PDB_Info.Kd_nM_ + " (BINDINGDB)"); ProcessRow(drug_information_result_url_row, drug_information_result_url, "Link to further drug information", "DrugInfoResult.aspx?query_string=" + drug.Drug_Name_for_Pull_Down_Menu); }
/// <summary> /// Author: Garth Nelson /// </summary> protected new void Page_Load(object sender, EventArgs e) { base.Page_Load(sender, e); SNV_ID_Key = Request.QueryString["query_string"]; try { string stringAfterPDot = SNV_ID_Key.Substring(SNV_ID_Key.IndexOf("p.") + 2); string specifiedAAType = new string(stringAfterPDot.TakeWhile(c => char.IsLetter(c)).ToArray()); string specifiedAANumber = new string(stringAfterPDot.Substring(specifiedAAType.Length).TakeWhile(c => char.IsNumber(c)).ToArray()); string specifiedAA = specifiedAAType + "-" + specifiedAANumber; mutations = EF_Data.GetMutationsBySNVIDKey(SNV_ID_Key); proteinMutation = EF_Data.GetMutationBySNVIDKey(SNV_ID_Key); protein = EF_Data.GetProteinByUniprotID(proteinMutation.UniProt_ID); foreach (SNV_Mutation mutation in mutations) { Drug_Information drug = EF_Data.GetDrugByDrugPDBID(mutation.Drug_PDB_ID); drugs.Add(drug); PDB_Interaction interaction = EF_Data.GetPDB_Interaction(mutation.UniProt_ID, mutation.Drug_PDB_ID, specifiedAA); interactions.Add(interaction); } Session["drugs"] = drugs; Session["interactions"] = interactions; Session["mutations"] = mutations; Session["SNV_ID_Key"] = SNV_ID_Key; LoadSNVID(SNV_ID_Key); LoadTargetGeneID(protein, mutations[0]); CreateIDofPDILinkedSNVTable(drugs, interactions, mutations); } catch (Exception) { Page.Master.FindControl("BodyContentPlaceHolder").Visible = false; ExceptionUtilities.DisplayAlert(this, QUERY_PAGE); } }
protected void LoadAminoAcidDropDown(object sender, EventArgs e) { amino_acid_specification_drop_down.Items.Clear(); amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); try { if (drug_specification_drop_down.SelectedItem.Value != DROP_DOWN_PROMPT_MESSAGE) { Protein_Information protein = EF_Data.GetProtein(search_textBox.Text); Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification_drop_down.SelectedItem.Value); PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug); List <SNV_Mutation> mutations = EF_Data.GetMutations(protein.UniProt_ID, drug.Drug_PDB_ID, PDB.PDB_File_ID); if (mutations.Count > 0) { List <string> dropdownValues = new List <string>(); foreach (SNV_Mutation mutation in mutations) { dropdownValues.Add(mutation.SNV_Key); } dropdownValues = DataUtilities.FilterDropdownList(dropdownValues); foreach (string dropdownValue in dropdownValues) { amino_acid_specification_drop_down.Items.Add(dropdownValue); } } else { amino_acid_specification_drop_down.Items.Clear(); amino_acid_specification_drop_down.Items.Add(DROP_DOWN_NO_MATCHES_MESSAGE); } } } catch (Exception) { amino_acid_specification_drop_down.Items.Clear(); amino_acid_specification_drop_down.Items.Add(DROP_DOWN_PROMPT_MESSAGE); } }
/// <summary> /// Author: Andy Tang /// </summary> public static PDB_Information GetPDBInfo(Protein_Information protein, Drug_Information drug) { PDB_Information PDBInfo = null; if (protein == null || drug == null) { return(PDBInfo); } using (DrugProNETEntities context = new DrugProNETEntities()) { PDBInfo = context.PDB_Information.Where(pdb => pdb.UniProt_ID.Equals(protein.UniProt_ID, StringComparison.OrdinalIgnoreCase) && pdb.Drug_PDB_ID.Equals(drug.Drug_PDB_ID, StringComparison.OrdinalIgnoreCase) ).FirstOrDefault(); } return(PDBInfo); }
/// <summary> /// Author: Andy Tang /// </summary> protected new void Page_Load(object sender, EventArgs e) { base.Page_Load(sender, e); string query = Request.QueryString["query_string"]; try { drug = EF_Data.GetDrugUsingDropDownName(query); if (drug != null) { LoadData(drug); } } catch (Exception) { throw; } }
/// <summary> /// Author: Andy Tang /// </summary> private void LoadData(Drug_Information drug) { ProcessRow(compound_name_row, compound_name, drug.Drug_Common_Name); ProcessRow(chemical_name_row, chemical_name, drug.Drug_Chemical_Name); ProcessRow(compound_alias_row, compound_alias, drug.Other_Drug_Name_Alias); ProcessRow(compound_inchl_row, compound_inchl_id, drug.Drug_InChl); ProcessRow(drug_formula_row, drug_formula, drug.Drug_Formula); ProcessRow(molecular_mass_row, molecular_mass, drug.Molecular_Mass); ProcessRow(pdb_drug_id_row, pdb_drug_id, drug.Drug_PDB_ID, drug.Drug_PDB_ID_URL); ProcessRow(compound_cas_id_row, compound_cas_id, drug.Compound_CAS_ID); ProcessRow(chembl_id_row, chembl_id, drug.ChEMBL_ID, drug.ChEMBL_Link); ProcessRow(kinase_sarfair_row, kinase_sarfair, drug.ChEMBL_ID, drug.CHEMBL_Kinase_SARFari_Link); ProcessRow(pubchem_sid_row, pubchem_sid, drug.PubChem_SID, drug.PubChem_Substance_Link); ProcessRow(pubchem_cid_row, pubchem_cid, drug.PubChem_CID, drug.PubChem_Compound_Link); ProcessRow(chemspider_sid_row, chemspider_sid, drug.ChemSpider_ID, drug.ChemSpider_Link); ProcessRow(chebi_id_row, chebi_id, drug.ChEBI_ID, drug.ChEBI_Link); ProcessRow(bindingdb_id_row, bindingdb_id, drug.BindingDB_ID, drug.BindingDB_Link); ProcessRow(drugbank_id_row, drugbank_id, drug.DrugBank_ID, drug.DrugBank_Link); ProcessRow(drug_reg_row, drug_registration, drug.Drug_Registration_Number); ProcessRow(kegg_drug_id_row, kegg_drug_id, drug.KEGG_Drug_ID, drug.KEGG_Drug_Link); ProcessRow(therapeautic_target_row, therapeutic_target_id, drug.Therapeutic_Targets_ID, drug.Therapeutic_Targets_Link); ProcessRow(pharmgkb_id_row, pharmgkb_id, drug.PharmGKB_ID, drug.PharmGKB_Link); ProcessRow(het_id_row, het_id, drug.HET_ID, drug.HET_Link); ProcessRow(drug_product_row, drug_product_id, drug.Drug_Product_ID, drug.Drug_Product_ID_Link); ProcessRow(rxlist_id_row, rxlist_id, drug.RxList_ID, drug.RxList_Link); ProcessRow(drugs_com_id_row, drugs_com_id, drug.Drugs_com_ID, drug.Drugs_com_Link); ProcessRow(wikipedia_row, wikipedia, drug.Wikipedia, drug.Wikipedia_Link); ProcessRow(general_activity_row, general_activity, drug.General_Activity); ProcessRow(general_targets_row, general_targets, drug.General_Targets); ProcessRow(commentary_row, commentary, drug.Commentary); ProcessRow(source_type_row, source_type, drug.Source_Type); ProcessRow(living1_source_row, living_source1, drug.Living_Source1); ProcessRow(living2_source_row, living_source2, drug.Living_Source2); ProcessRow(approved_row, clinically_approved, drug.Clinically_Approved); ProcessRow(latest_stage_trial_row, latest_stage_trials, drug.Latest_Stage_Trials); ProcessRow(producer_row, producer, drug.Producer); ProcessRow(disease_applications_row, disease_applications, drug.Disease_Applications); ProcessRow(toxic_effects_row, toxic_effects, drug.Toxic_Effects); ProcessRow(reference1_row, reference_1, drug.Reference_1); ProcessRow(reference2_row, reference_2, drug.Reference_2); }
/// <summary> /// Author: Garth Nelson /// </summary> protected new void Page_Load(object sender, EventArgs e) { base.Page_Load(sender, e); try { string protein_specification = Request.QueryString["query_string"]; string drug_specification = Request.QueryString["drug_specification"]; string SNV_Key = Request.QueryString["snv_id_key"]; Session["SNV_Key"] = SNV_Key; Protein_Information protein = EF_Data.GetProtein(protein_specification); Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification); PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug); string[] SNV_KEYsplit = SNV_Key.Split('-'); // Retrieve second and third elements string amino_acid_specification = SNV_KEYsplit[1] + "-" + SNV_KEYsplit[2]; PDB_Interaction interaction = EF_Data.GetPDB_Interaction(protein.Uniprot_ID, drug.Drug_PDB_ID, amino_acid_specification); mutation = EF_Data.GetMutationBySNVKey(SNV_Key); Session["mutation"] = mutation; LoadProtein(protein, interaction, mutation); LoadDrug(drug, mutation); LoadPDB_Info(PDB); CreateSNVIdentificationTable(mutation); } catch (Exception) { Page.Master.FindControl("BodyContentPlaceHolder").Visible = false; ExceptionUtilities.DisplayAlert(this, QUERY_PAGE); } }
/// <summary> /// Author: Andy Tang, Ryan Liang /// </summary> protected new void Page_Load(object sender, EventArgs e) { base.Page_Load(sender, e); if (!IsPostBack) { string fromPage = null; string query_string = null; try { query_string = Request.QueryString["query_string"]; drug_specification = Request.QueryString["drug_specification"]; protein_specification = Request.QueryString["protein_specification"]; if (!string.IsNullOrEmpty(drug_specification)) { protein_specification = query_string; fromPage = "protein"; } else if (!string.IsNullOrEmpty(protein_specification)) { drug_specification = query_string; fromPage = "drug"; } drug = EF_Data.GetDrugsQuery(drug_specification).FirstOrDefault(); protein = EF_Data.GetProteinsInfoQuery(protein_specification).FirstOrDefault(); PDB = EF_Data.GetPDBInfo(protein, drug); Session["PDB_File_ID"] = PDB.PDB_File_ID; interaction_distance = double.Parse(Request.QueryString["interaction_distance"]); protein_chain = bool.Parse(Request.QueryString["protein_chain"]); protein_atoms = bool.Parse(Request.QueryString["protein_atoms"]); protein_residues = bool.Parse(Request.QueryString["protein_residues"]); protein_residue_numbers = bool.Parse(Request.QueryString["protein_residue_numbers"]); drug_atoms = bool.Parse(Request.QueryString["drug_atoms"]); Session["interaction_distance"] = interaction_distance; } catch (Exception) { throw; } if (drug == null || protein == null || PDB == null) { Page.Master.FindControl("BodyContentPlaceHolder").Visible = false; if (fromPage != null) { ExceptionUtilities.DisplayAlert(this, fromPage.Equals("drug") ? DRUG_QUERY_PAGE : PROTEIN_QUERY_PAGE); } else { ExceptionUtilities.DisplayAlert(this, DEFAULT_REDIRECT_PAGE); } } else { Session["interaction_distance"] = interaction_distance; Session["protein_chain"] = protein_chain; Session["protein_atoms"] = protein_atoms; Session["protein_residues"] = protein_residues; Session["protein_residue_numbers"] = protein_residue_numbers; Session["drug_atoms"] = drug_atoms; LoadProtein(protein); LoadDrug(drug, PDB); LoadPDB_Info(PDB); GetDrugAtomNumberingImage(drug); CreateInteractionList(PDB, interaction_distance, protein_chain, protein_atoms, protein_residues, protein_residue_numbers, drug_atoms); CreateInteractionSummary(); ScriptManager.RegisterStartupScript(Page, GetType(), "D_3DViewer", "javascript:loadDrugLigand('" + drug.Drug_PDB_ID + "');", true); ScriptManager.RegisterStartupScript(Page, GetType(), "PDB_3DViewer", "javascript:loadStage('" + drug.PDB_File_ID + "', '" + drug.Drug_PDB_ID + "');", true); } } }
/// <summary> /// Author: Ryan Liang /// </summary> private void GetDrugAtomNumberingImage(Drug_Information drug) { selected_amino_acid_residue_atom_numbering.ImageUrl = "https://cdn.rcsb.org/images/ligands/" + drug.Drug_PDB_ID.Substring(0, 1) + "/" + drug.Drug_PDB_ID + "/" + drug.Drug_PDB_ID + "-large.png"; }