Usage: /services/aa_info.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns name and pdbid of all viruses in the database. It doesn't requiere any parameters.
/services/aa_info.php?serviceName=viruses
[{entry_id:1rb8,name:Φ-X 174 DNA binding protein J},{entry_id:3rqv,name:1.45 ANGSTROM STRUCTURE OF STNV COAT PROTEIN}...]
Returns all the codon triplet of the amino acids (residues) that compose the capsid. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/aa_info.php?serviceName=aminos&VDB=2bbv
[{label_comp_id:ADE},{label_comp_id:ALA},...]
Returns the ID of the sequence where the amino acid (residue) appears in the chain (protein). VDB means PDBID (Protein Data Bank Identifier), labelcompid means codon triplet of amino acid (residue).
VDB,labelcompid
/services/aa_info.php?serviceName=residues&VDB=2bbv&labelcompid=ALA
[{label_comp_id:ALA,label_seq_id:23},{label_comp_id:ALA,label_seq_id:55},...]
Returns details about any residue such as its type. VDB means PDBID (Protein Data Bank Identifier), labelcompid means codon triplet of amino acid (residue), labelseqid means the sequence where the amino acid (residue) appears in the chain (protein).
VDB,labelcompid,labelseqid
/services/aa_info.php?serviceName=tableAmino&VDB=2bbv&labelcompid=ALA&labelseqid=23
{name:Black Beetle Virus (BBV),entry_id:2bbv,amino:ALA,aminoname:Alanine,aminortype:H,aminotype:Hydrophobic,numcontacts:2,sic:Interface Residue}
Returns values of information on buried surface areas and association energies. VDB means PDBID (Protein Data Bank Identifier), labelcompid means codon triplet of amino acid (residue), labelseqid means the sequence where the amino acid (residue) appears in the chain (protein).
VDB,labelcompid,labelseqid
/services/aa_info.php?serviceName=tableBSAAE&VDB=2bbv&labelcompid=ALA&labelseqid=23
[{viper_residue_asa_key:1173902,entry_key:163,entry_id:2bbv,layer_key:null,layer_name:null,label_comp_id:ALA,label_seq_id:23,label_asym_id:A,sasa_bound:11.3999996185303,sasa_unbound:88.5999984741211,sasa_reference_aa:240.699996948242,delta_sasa:-77.1999969482422,delta_sasa_polar:-9.39999961853027,delta_sasa_nonpolar:-67.8000030517578,solvE_polar:0.0850000008940697,solvE_nonpolar:-1.22000002861023,solvE_total:-1.1360000371933,asscnE_polar_hn:-0.101999998092651,asscnE_nonpolar_hn:-1.70899999141693,asscnE_total:-1.81099998950958,radius_aa:125.300003051758,radius_max:170.889999389648,radius_min:102.430000305176,radius_range:68.4599990844727,eff_rad_x_sasa_min:259.399993896484,expsd_aa_charge:0,expsd_aa_charge_sum:0,num_sidechain_atoms:2}]
Returns contact information about any virus with a chain and a sequence selected. VDB means PDBID (Protein Data Bank Identifier), labelcompid means codon triplet of amino acid, labelseqid means the sequence where the amino acid (residue) appears in the chain.
VDB,labelcompid,labelseqid
/services/aa_info.php?serviceName=tableContacs&VDB=2bbv&labelcompid=ALA&labelseqid=23
[{contacts:ALA23 : ALA361,interface:A1 : C6,type:H : H,bsa:77.24 : 32.12,assoenergy:-1.81 : -0.81,solvenergy:-1.14 : -0.58},...]
Returns the chain or chains what amino acid (residue) belongs. VDB means PDBID (Protein Data Bank Identifier), labelcompid means codon triplet of amino acid (residue), labelseqid means the sequence where the amino acid (residue) appears in the chain (protein).
VDB,labelcompid,labelseqid
/services/aa_info.php?serviceName=chains&VDB=2bbv&labelcompid=ALA&labelseqid=23
[A]
Calculates all the coordinates of the amino acids (residues) located in the range of the selected radius. Makes a .vdb file and provide a link to access it. VDB means PDBID (Protein Data Bank Identifier), seq means the sequence where the amino acid (residue) appears in the chain (protein), chain means the protein what amino acid (residue) belongs, radius means the distance between others amino acids (residues) and the amino acid (residue) selected.
VDB,seq,chain,radius
/services/aa_info.php?serviceName=results&VDB=2bbv&seq=23&chain=A&radius=10
{link:../TEMP/57501.vdb}
Usage: /services/accessible_surface_profiles.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all amino acids (residues) contained in each chain (protein) and their sequence, triplet and the parameters (effective radius and min solvent accessible surface area), as well as(effective radius * min solvent accessible surface area). VDB means PDBID (Protein Data Bank Indentifier).
serviceName, VDB
/services/accessible_surface_profiles.php?serviceName=residues&VDB=2bbv
[{"entry_id":"2bbv","label_asym_id":"A","residue":[{"label_seq_id":20,"label_comp_id":"THR","sasa_min":120,"effective_radius":15,"effradXsamin":1755},...]},...]
Usage: /services/contact_finder.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all families registered in the database. It doesn't have parameters.
/services/contact_finder.php?serviceName=families
[{family:Adenoviridae},{family:Astroviridae},...]
Returns all genus that belong to a selected family. family means the family that some virus belongs.
family
/services/contact_finder.php?serviceName=genus&family=Adenoviridae
[{genus:Mastadenovirus}]
Returns all triplet (identifier of an amino acid) that could be belong to a chain (protein). It doesn't have parameters.
/services/contact_finder.php?serviceName=residue1
[{auth_1_comp_id:ADE},{auth_1_comp_id:ALA},...]
Returns all triplet (identifier of an amino acid) that could be belong to a chain (protein). It doesn't have parameters.
/services/contact_finder.php?serviceName=residue2
[{auth_2_comp_id:ADE},{auth_2_comp_id:ALA},...]
Returns all PDBID (Protein Data Bank Identifier) that belong to a family and a genus selected. family means the family that some virus belongs, genus means the genus that some virus belongs.
family,genus
/services/contact_finder.php?serviceName=entries&family=Adenoviridae&genus=Mastadenovirus
[{entry_id:1vsz},{entry_id:1x9p},...]
Returns all amino acids (residues) nearest to selected amino acids (residues) with their triplet and sequence. family means the family that some virus belongs, genus means the genus that some virus belongs, VDB means PDBID (Protein Data Bank Identifier), res1 and res2 means a triplet each, resnum1 and resnum2 means the sequence, mindist and maxdist means a range stablished between amino acids (residues) selected and amino acids (residues) serched. Almost all parameters can be NULLS.
family,genus,VDB,res1,res2,resnum1,resnum2,mindist,maxdist
/services/contact_finder.php?serviceName=finder&family=Adenoviridae&genus=Mastadenovirus&VDB=1x9p
[{entry_id:1x9p,res1:ALA,rednum1:465,res2:ILE,resnum2:560,ch1ch2:A1:A2,intsym:I:5,distance:5.16389989852905,assocenergies:-1.25:-0.93},...]
Usage: /services/contact_table.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns a table with all the possible residue pairs that contact at the subunit (chain or protein) interfaces are listed in the first column. These are listed in the increasing order of the first residue number (Residue1). VDB means PDBID (Protein Data Bank Identifier), layer means a section such as INNER, OUTER or COMPLETE. layer can be NULL.
VDB,layer
/services/contact_table.php?serviceName=contactst1&VDB=2bbv
[{r1r2:CYT2-URA8,t1t2:NA-NA,R1_R6_I_0:R1-R6,A1_B7_Q_0:*,R1_C1_Q_0:*,R6_C1_Q_0:*,C1_C6_I_2:*,A2_B1_Q_2:*,A1_A3_I_3:*,B1_B7_I_3:*,C1_C16_I_3:*,A1_B1_Q_3:*,A1_C1_Q_3:*,C1_B1_Q_3:*,A2_A1_I_5:*,B1_C2_Q_5:*,A1_C6_Q_6:*,C6_B1_Q_6:*},...]
Returns a table with the total of interfaces and the unique interfaces counted. VDB means PDBID (Protein Data Bank Identifier), layer means a section such as INNER, OUTER or COMPLETE. layer can be NULL.
VDB,layer
/services/contact_table.php?serviceName=contactst2&VDB=2bbv
{uniques:{R1_R6_I_0:32,A1_B7_Q_0:1,C1_R1_Q_0:32,C1_R6_Q_0:11,C1_C6_I_2:20,A2_B1_Q_2:22,A1_A3_I_3:1,B1_B7_I_3:1,C1_C16_I_3:1,A1_B1_Q_3:82,A1_C1_Q_3:75,B1_C1_Q_3:78,A1_A2_I_5:21,B1_C2_Q_5:22,A1_C6_Q_6:21,B1_C6_Q_6:31},intuniques:[{NA_NA:32,NA_H:0,NA_P:0,NA_A:0,NA_B:0,H_NA:0,H_H:0,H_P:0,H_A:0,H_B:0,P_NA:0,P_H:0,P_P:0,P_A:0,P_B:0,A_NA:0,A_H:0,A_P:0,A_A:0,A_B:0,B_NA:0,B_H:0,B_P:0,B_A:0,B_B:0},...]
Usage: /services/database_browser.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all tables of VIPERdb.
/services/database_browser.php?serviceName=viperTables
[{table:MSA_Family,description:,category_key:},{table:MSA_Structure_Based_Advanced_Details,description:,category_key:}...]
Returns all tables of MMS.
/services/database_browser.php?serviceName=mmsTables
[{table:ATOM_SITE,description:Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions, and so on. The data items for describing anisotropic temperature or atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category.,category_key:0},...]
Executes any query and returns results. THIS IS VERY DANGEROUS. This service should be only used for get results of SELECT QUERIES.
query
/services/database_browser.php?serviceName=
query
Usage: /services/energy_list.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all families registered in the database with some exceptions (considering the superecede). It doesn't have parameters.
/services/energy_list.php?serviceName=famlist
[{family:Adenoviridae},{family:Birnaviridae},...]
Returns all interface association energies of the selected family. family means the family that some virus belongs
family
/services/energy_list.php?serviceName=interfaceTable&family=Adenoviridae
[{entry_id:3iyn,genus:Mastadenovirus,tnumber:pT25,title:3.6-Angstrom cryoEM structure of human adenovirus type 5,interfaces:{A1_A2:{interface:A1_A2,assocn_nrg_total:},...}]
Usage: /services/energy_table.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the association energy data table. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/energy_table.php?serviceName=energy&VDB=2bbv
[{interface_name:A1-B1,interface_type:Q-3,assocn_nrg_total:-85.7,bsa_total:4233.4,solvn_nrg_total:-21.3},...]
Returns all energy association located from an interface to other. VDB means PDBID (Protein Data Bank Identifier), face means interfaces selected with energy association, data means if we want Association Energy (kcal/mol), Buried Surface Area or Solvation Energy (kcal/mol).
VDB,face,data
/services/energy_table.php?serviceName=energyPlot&VDB=2bbv&face=A1-B1&data=association_nrg
[[{entry_id:2bbv,MAX:379,MIN:20,FL:[{auth_1_seq_id:20,auth_1_comp_id:THR,association_nrg:0.00},...]}]]
Returns all contacts of some virus on the selected interace. VDB means PDBID (Protein Data Bank Identifier), face means interfaces selected with energy association, auth_1_seq_id means the sequence where the amino acid (residue) appears in the chain (protein), order means if starts with the first residue to second residue or upside down.
VDB,face,auth_1_seq_id,order
/services/energy_table.php?serviceName=contacts&VDB=2bbv&face=A1-B1&auth_1_seq_id=248&order=1
[{entry_id:2bbv,auth_1_seq_id:248,auth_1_comp_id:PRO,auth_2_seq_id:167,auth_2_comp_id:ARG,association_nrg:-2.99,bsa:129.66,solvation_nrg:-1.81,con_association_nrg:-0.01,con_bsa:1.26,con_solvation_nrg:0.01,difAnrg:-1.5,difbsa:65.46,difSnrg:-0.9},...]
Usage: /services/family_index.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all families registered in the database excepting familes with superecede NULL. It doesn't have parameters.
/services/family_index.php?serviceName=families
[{family:Adenoviridae},{family:Birnaviridae},...]
Returns all viruses that belong to a selected family. family means the family that some virus belongs.
family
/services/family_index.php?serviceName=family_members&family=Adenoviridae
[{entry_id:3iyn,name:3.6-Angstrom cryoEM structure of human adenovirus type 5,genus:Mastadenovirus,resolution:3.60,tnumber:pT25},...]
Usage: /services/featured_entries.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the 10 lastest entries registered. It doesn't have parameters.
/services/featured_entries.php?serviceName=lastest_entries
[{entry_id:5foj,name:ELECTRON CRYO-MICROSCOPY OF GRAPEVINE FANLEAF VIRUS COMPLEX WITH NANOBODY,deposition_date:2015-11-22},...]
Returns the 10 most viewed entries registered. It doesn't have parameters.
/services/featured_entries.php?serviceName=popular_entries
[{entry_id:1x9p,name:Human Adenovirus 2 Penton Base,times_viewed:19004},...]
Returns the total visits, visits of last month, the number of entries registered, the total families and total genus. The counter of visits was replaced and the results gotten from this services can change. It doesn't have parameters.
/services/featured_entries.php?serviceName=data_entries
{visits_last_month:4257,total_entries:[{COUNT(DISTINCT entry_key):503}],families:[{COUNT(DISTINCT family):39}],genera:[{COUNT(DISTINCT genus):79}]}
Returns all viruses that contain in their PDBID the characters digited by the user. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/featured_entries.php?VDB=2b
[{entry_id:2bbv,name:Black Beetle Virus (BBV)},{entry_id:2bpa,name:Bacteriophage Φ-X 174},{entry_id:2btv,name:Bluetongue Virus},{entry_id:2bu1,name:Bacteriophage MS2/RNA Hairpin (5bru-5) Complex},...]
Returns all viruses that contain in their name the characters digited by the user. VDB means PDBID (Protein Data Bank Identifier).
title
/services/featured_entries.php?title=black
[{entry_id:2bbv,name:Black Beetle Virus (BBV)}]
Usage: /services/gallery_maker.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all families registered in the database. It doesn't have parameters.
/services/gallery_maker.php?serviceName=families
[{family:Adenoviridae},{family:Birnaviridae},...]
Returns all genus registered in the database. It doesn't have parameters.
/services/gallery_maker.php?serviceName=genus
[{genus:Alfamovirus},{genus:Allolevivirus},...]
Returns all viruses registered in the database. It doesn't have parameters.
/services/gallery_maker.php?serviceName=entries
[{name:Φ-X 174 DNA binding protein J,entry_id:1rb8},{name:1.45 ANGSTROM STRUCTURE OF STNV COAT PROTEIN,entry_id:3rqv},{name:1.45 ANGSTROM STRUCTURE OF STNV COAT PROTEIN,entry_id:4v4m},...]
Returns all releated viruses with the characteristics selected. families means the families that some virus belongs, genus means the genus that some virus belongs, VDBs means PDBID (Protein Data Bank Identifier), nonredundant, method, ordersize, oneperfam.
families,genus,VDBs,nonredundant,method,ordersize,oneperfam
/services/gallery_maker.php?serviceName=galleryMaker
[{entry_id:2gsy,name:THE 2.6A STRUCTURE OF INFECTIOUS BURSAL VIRUS DERIVED T=1 PARTICLES,family:Birnaviridae,genus:Avibirnavirus,ave_diameter:262,tnumber:1,method:X-RAY DIFFRACTION},{entry_id:3ide,name:STRUCTURE OF IPNV SUBVIRAL PARTICLE,family:Birnaviridae,genus:Aquabirnavirus,ave_diameter:264,tnumber:1,method:X-RAY DIFFRACTION},...]
Usage: /services/genus_index.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all genus registered in the database. It doesn't have parameters.
/services/genus_index.php?serviceName=genus
[{genus:Alfamovirus},{genus:Allolevivirus},...]
Returns all viruses that belong to a selected genus. genus means the genus that some virus belongs.
genus
/services/genus_index.php?serviceName=genus_members&genus=Alfamovirus
[{entry_id:amv,name:Alfalfa Mosaic Virus,family:Bromoviridae,genus:Alfamovirus,resolution:4.00,tnumber:1}]
Usage: /services/hetero.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all hetero groups in virus structures. It doesn't have parameters.
/services/hetero.php?serviceName=hetero
[{name:Poliovirus (Type 1, Mahoney Strain) Mutant V1160I,entry_id:1al2,family:Picornaviridae,tnumber:pT3,RDNA:-,water:[534],ions:-,other:[1 SPH,1 MYR],resolution:2.90},{name:Bacteriophage MS2 Mutant (T59S)/RNA Operator,entry_id:1aq3,family:Leviviridae,tnumber:3,RDNA:[{color:BLUE,entity_nmol:2 (RNA),pdbx_seq_one_letter_code:ACAUGAGGAUUACCCAUGU}],water:[216],ions:-,other:-,resolution:2.80},...]
Usage: /services/mapares.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns name, PDBID and t-number of all viruses or name and PDBID if input the parameter VDB. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/mapares.php?serviceName=capsids
[{name:Φ-X 174 DNA binding protein J,entry_id:1rb8,tnumber:1},...]
Usage: /services/mat.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all matrix numbers that place the asymmetric unit in the capsid. The numbering of asymmetric units for other T-number cages is the same as that of the T=1 cage.
/services/mat.php?serviceName=matrix
[{icos_matrix_key:1,matrix_0_0:1.00000,matrix_0_1:0.00000,matrix_0_2:0.00000,matrix_1_0:0.00000,matrix_1_1:1.00000,matrix_1_2:0.00000,matrix_2_0:0.00000,matrix_2_1:0.00000,matrix_2_2:1.00000,vector_0:0.00000,vector_1:0.00000,vector_2:0.00000},...]
Usage: /services/msa_family.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the alignment where appears the selected virus. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/msa_family.php?serviceName=msa&VDB=2bbv
[{Family_name:Nodaviridae,Id_MSSA_Align:6}]
Usage: /services/oligomer.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the routes of generated files. The files generated are a .PDB and .TAR.GZ.
VDB,layer,alpha,particle,modeller,matx
/services/oligomer.php?serviceName=oligomerMaker&VDB=2bbv&layer=&alpha=yes&particle=&modeller=60mer&matx=1-10
{route:out_3374.pdb,compress:out_3374.tar.gz}
Usage: /services/oligomer_multi.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns name, PDBID (Protein Data Bank Identifier) and the highest t-number of all viruses.
/services/oligomer_multi.php?serviceName=capsids
[{name:MPCV2,entry_id:0mpcv2,tnumber:1},{name:SS-MODEL of PCV2,entry_id:0pcv2,tnumber:1},...]
Returns name, PDBID (Protein Data Bank Identifier) and the highest t-number of a selected virus. VDB means PDBID.
VDB
/services/oligomer_multi.php?serviceName=capsidVDB&VDB=2bbv
[{name:Black Beetle Virus (BBV),entry_id:2bbv,tnumber:3}]
Returns all chains (proteins) that belong to a selected virus. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/oligomer_multi.php?serviceName=lai&VDB=2bbv
[{label_asym_id:A},{label_asym_id:B},{label_asym_id:C},{label_asym_id:R}]
Usage: /services/qscores.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the Q-scores of some virus selected. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/qscores.php?serviceName=scores&VDB=2bbv
[{face_1_asym_id_1:B,face_1_matrix_1:1,face_1_asym_id_2:C,face_1_matrix_2:1,:::,face_2_asym_id_1:A,face_2_matrix_1:1,face_2_asym_id_2:B,face_2_matrix_2:1,face_1_type:Q,face_1_symm:3,face_2_type:Q,face_2_symm:3,shared:72,numcon_1:78,numcon_2:80,qscore:0.911391973495483},...]
Usage: /services/related_viruses.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all viruses that belong to a selected family. family means the family that some virus belongs.
family
/services/related_viruses.php?serviceName=byfamily&family=Adenoviridae
[{entry_id:1x9p,name:Human Adenovirus 2 Penton Base},{entry_id:1x9t,name:Human Adenovirus 2 Penton Base In Complex With An Ad2 N-Terminal Fibre Peptide},...]
Returns all viruses that belong to a selected genus. genus means the genus that some virus belongs.
genus
/services/related_viruses.php?serviceName=bygenus&genus=Alfamovirus
[{entry_id:amv,name:Alfalfa Mosaic Virus}]
Usage: /services/rna.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the ordered portions of nucleic acid (DNA or RNA)for each family. It doesn't have parameters.
/services/rna.php?serviceName=fullRNA
[{family:Bromoviridae,members:[{name:Cowpea Chlorotic Mottle Virus (CCMV),types:RNA,sequences:R(AUAU), T(AU),lengths:R(4), T(2),entry_id:1cwp},{...}}]
Returns the stereo pics for each virus found. It doesn't have parameters.
/services/rna.php?serviceName=stereoPics
[{name:Cowpea Chlorotic Mottle Virus (CCMV),entry_id:1cwp,stereo:rna_1cwp_stereo.gif,mono:rna_1cwp.gif},...]
Usage: /services/ss_info.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns name and PDBID (Protein Data Bank Identifier) of all viruses registered. It doesn't have parameters.
/services/ss_info.php?serviceName=virus
[{entry_id:1a6c,name:Tobacco Ringspot Virus},{entry_id:1al0,name:PROCAPSID OF BACTERIOPHAGE PHIX174},...]
Returns all chains (proteins) that belong to some virus, and their biggest and small sequences. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/ss_info.php?serviceName=chain&VDB=2bbv
[{label_asym_id:A,MINlsi:20,MAXlsi:379},{label_asym_id:B,MINlsi:56,MAXlsi:379},{label_asym_id:C,MINlsi:55,MAXlsi:379}]
Returns data about residues placed in the range that we established. VDB means PDBID (Protein Data Bank Identifier), asym means the chain (protein) that belongs to a some virus, asymstart means the sequece where is placed any amino acid (residue), this is te initial value of range, asymend means the sequece where is placed any amino acid (residue), this is te final value of range.
VDB,asym,asymstart,asymend
/services/ss_info.php?serviceName=range&VDB=2bbv&asym=A&asymstart=20&asymend=379
[{id:2725,label_atom_id:N,auth_comp_id:SER,label_asym_id:A,auth_seq_id:350,cartn_x:7.00002002716064,cartn_y:44.8386001586914,cartn_z:115.667999267578,occupancy:1,b_iso_or_equiv:15},...]
Returns the sequences that belong to the secondary structure of some virus and highlights their secondary structure key and their residue type. VDB means PDBID (Protein Data Bank Identifier), asym means the chain (protein) that belongs to a some virus, asymstart means the sequece where is placed any amino acid (residue), this is te initial value of range, asymend means the sequece where is placed any amino acid (residue), this is te final value of range.
VDB,asym,asymstart,asymend
/services/ss_info.php?serviceName=sequence&VDB=2bbv&asym=A&asymstart=20&asymend=379
[{label_seq_id:20,res_type:P,comp_id:THR,color:darkorchid,name:T,struct:C},{label_seq_id:21,res_type:P,comp_id:GLN,color:darkorchid,name:Q,struct:C},...]
Usage: /services/stats.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the number of all registered entries and also how much viruses was gotten for each method (Cryo Em or X Ray). It doesn't have parameters.
/services/stats.php?serviceName=entriesAll
[{total_entries:503},{numCryoem:143},{numXray:354},{numTheore:6}]
Returns the sum of Cryo Ems or X Ray methods made each year. It doesn't have parameters.
/services/stats.php?serviceName=xrayvcryo
[{Year:1984,CryoEM:0,Xray:1},{Year:1985,CryoEM:0,Xray:1},...]
Returns the resolution for each method (Cryo Em or X Ray) in each time that was made. It doesn't have parameters.
/services/stats.php?serviceName=resxraycryo
{resCryoEM:[{resolution:5.70,deposition_date:0000-00-00},...]}
Returns the diameters average for each method (Cryo Em or X Ray) in each time that was made. It doesn't have parameters.
/services/stats.php?serviceName=diamxraycryo
{diamCryoEM:[{ave_diameter:640,deposition_date:0000-00-00},{ave_diameter:358,deposition_date:1997-12-12}...]}
Returns the t-numbers for each method (Cryo Em or X Ray) in each time that was made. It doesn't have parameters.
/services/stats.php?serviceName=tnumxraycryo
{tnumberCryoEM:[{tnumber:7l,deposition_date:0000-00-00},{tnumber:1,deposition_date:1997-12-12},...]}
Returns all generic or helical families and their members number. It doesn't have parameters.
/services/stats.php?serviceName=entriesFamily
[{label:Corticoviridae,value:1},{label:Thermococcaceae,value:1},...]
Returns all generic or helical hosts and their members number. It doesn't have parameters.
/services/stats.php?serviceName=entriesHost
[{label:Nematode,value:1},{label:Fungi,value:1},...]
Usage: /services/structures.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns some viruses whose was solved by X Ray method. It doesn't have parameters.
/services/structures.php?serviceName=xray
[{entry_id:1rb8,pdb_id:1rb8,name:Φ-X 174 DNA binding protein J},{entry_id:4v4m,pdb_id:4v4m,name:1.45 ANGSTROM STRUCTURE OF STNV COAT PROTEIN},...]
Returns some viruses whose was solved by Cryo Em method. It doesn't have parameters.
/services/structures.php?serviceName=cryoem
[{entry_id:3izx,pdb_id:3izx,name:3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus},{entry_id:3iyn,pdb_id:3iyn,name:3.6-Angstrom cryoEM structure of human adenovirus type 5},...]
Returns some viruses whose was solved by MODEL method. It doesn't have parameters.
/services/structures.php?serviceName=model
[{entry_id:1l0t,pdb_id:1l0t,name:ATOMIC MODEL OF THE PAPILLOMAVIRUS CAPSID},{entry_id:ccmv_swln_1,pdb_id:null,name:CCMV Swollen Form Model 1},...]
Returns helical viruses. It doesn't have parameters.
/services/structures.php?serviceName=helical
[{entry_id:5a2t,pdb_id:5a2t,name:Bamboo mosaic virus},{entry_id:4udv,pdb_id:4udv,name:Cryo-EM structure of TMV at 3.35 A resolution},...]
Returns generic (non icosahedral) viruses. It doesn't have parameters.
/services/structures.php?serviceName=nonicosahedral
[{entry_id:5j09,pdb_id:5j09,name:CRYSTAL STRUCTURE OF DECAMERIC BFDV CAPSID PROTEIN},{entry_id:5j7v,pdb_id:5j7v,name:Faustovirus major capsid protein}]
Usage: /services/tnumber_index.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns all registered t-numbers. It doesn't have parameters.
/services/tnumber_index.php?serviceName=tnumbers
[{tnumber:1},{tnumber:13},{tnumber:2},{tnumber:3},{tnumber:4},...]
Returns all viruses whose have a selected t-number. tnumber means the number of chains (proteins) that compose the capsid.
tnumber
/services/tnumber_index.php?serviceName=tnumber_members&tnumber=1
[{entry_id:2c9g,name:Adenovirus Type 2 Penton Base Dodecahedron,family:Adenoviridae,genus:Mastadenovirus,resolution:null},...]
Returns viruses ordered by each family and t-number. tnumber means the number of chains (proteins) that compose the capsid, tnumber can be null.
tnumber
/services/tnumber_index.php?serviceName=familiesAndtnumbers
{Adenoviridae:[{name:3.6-Angstrom cryoEM structure of human adenovirus type 5,genus:Mastadenovirus,family:Adenoviridae,resolution:3.60,entry_id:3iyn},{name:Adenovirus Type 2 Penton Base Dodecahedron,genus:Mastadenovirus,family:Adenoviridae,resolution:null,entry_id:2c9g},...]}
Usage: /services/xtals.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the crystal information. It doesn't have parameters.
/services/xtals.php?serviceName=xtalinfo
[{vipPDB:1lp3,name:Adeno-Associated Virus,family:Parvoviridae,tnumber:1,Space_Group:P1,Unit_Cell1:249.690,Unit_Cell2:249.690,Unit_Cell3:644.760,Unit_Cell4:90.00,Unit_Cell5:101.16,Unit_Cell6:120.00,Particles_In_UnitCell:3,R_Factor:0.338,info_ref:1},...]
Returns the Space Group Frequencies for all registered entries in Viperdb. It doesn't have parameters.
/services/xtals.php?serviceName=spgrp
[{space_group_name_h_m:C 1 2 1,cell_setting:monoclinic,int_tables_number:5,count:26},{space_group_name_h_m:C 2 2 21,cell_setting:orthorhombic,int_tables_number:20,count:5},...]
Returns the sum of Frequencies of Space Groups. It doesn't have parameters.
/services/xtals.php?serviceName=frec
[{sgn:587}]
Returns Inter-Particle Contacts in Virus Crystals. It doesn't have parameters.
/services/xtals.php?serviceName=contacts
[{entry_id:1a6c,name:Tobacco Ringspot Virus},{entry_id:1asj,name:Poliovirus (Type 1, Mahoney Strain)},...]
Returns the crystal contacts of a selected virus. VDB means PDBID (Protein Data Bank Identifier).
VDB
/services/xtals.php?serviceName=xtalfull&VDB=2bbv
{resolution:2.80,VDB:2bbv,spgrp:P4232,unitcell1:362,unitcell2:362,unitcell3:362,unitcell4:90,unitcell5:90,unitcell6:90,conditions:Crystals grown at 20 ° C using hanging drop vapor diffusion method. A virus solution was prepared at 8 mg/ml using sodium phosphate buffer in a pH range of 6.9 to 7.2. The reservoir solution contained 0.55 M ammonium sulfate in 0.05 M sodium phosphate buffer adjusted to the same pH as the solution containing the virus. 5 µl of virus solution were mixed with 5 µl of reservoir solution and the mixture was equilibrated with 1 ml of the reservoir solution. The crystals would grow more rapidly if the reservoir and virus solution were initially made 1 and 0.5% (W/V) respectively in PEG 8000.,condref:11,inforef:81,tnumber:3}
Returns conditions.
/services/xtals.php?serviceName=xtal
[{vipPDB:1lp3,name:Adeno-Associated Virus,Conditions:Crystallization was by vapor diffusion with AAV at approx. 8.5 mg/ml in 25% glycerol, equilibrated against a reservoir also containing 4-5% polyethylene glycol 6000.,cond_ref:1},...]
Usage: /services/ipactivitylog.php?serviceName=SomeOption¶ms=SomeValue
Options
Returns the number of sessions registered. Each session means a visit.
/services/ipactivitylog.php?serviceName=visitsCount
[{visits:333}]
Returns the number of registered IP since the first was registered.
/services/ipactivitylog.php?serviceName=usersCount
[{users:145,since:2018-06-12}]
Returns the different countries from we have visited.
/services/ipactivitylog.php?serviceName=countryCount
[{countries:Brazil},{countries:China},{countries:Finland},{countries:France},{countries:Germany},{countries:Malaysia},{countries:Mexico},{countries:Montenegro},{countries:Norway},{countries:Peru},{countries:Romania},{countries:Russian Federation},{countries:Singapore},{countries:Slovenia},{countries:Spain},{countries:Sweden},{countries:Thailand},{countries:Ukraine},{countries:United Kingdom},{countries:United States},{countries:Uzbekistan}]
Returns visits per day that we have had.
/services/ipactivitylog.php?serviceName=visitsPerDay
[{Year:2018,Month:6,Day:12,Visits:6},{Year:2018,Month:6,Day:13,Visits:4},{Year:2018,Month:6,Day:14,Visits:3},...]
Returns visits per month that we have had.
/services/ipactivitylog.php?serviceName=visitsPerMonth
[{Year:2018,Month:6,Visits:27},{Year:2018,Month:7,Visits:83},{Year:2018,Month:8,Visits:144},{Year:2018,Month:9,Visits:79}]
Returns visits per year that we have had.
/services/ipactivitylog.php?serviceName=visitsPerYear
[{Year:2018,Visits:333}]
Returns visits that we have had in a selected year and a selected month.
year,month
/services/ipactivitylog.php?serviceName=visitsMonth&year=2018&month=8
{Year:2018,Month:8,Visits:144}