antimicrobial peptides ( amps ) are host defense molecules universal in the innate immune systems of both invertebrates and vertebrates . because these ancient molecules remain potent after millions of years , they are regarded as important templates for developing a new generation of antimicrobials to combat antibiotic resistant superbugs , hiv-1 and cancer ( 19 ) . a clear growth of amp research started in the 1980s owing to the discoveries of insect cecropins by hans boman , human -defensins by robert lehrer and magainins by michael zasloff ( 1012 ) . it is now accepted that the functional roles of amps are not limited to antimicrobial . natural amps can have other functions such as apoptosis , wound healing and immune modulation . in addition , a balanced expression of amps is so important that either under or over - expression is related to human diseases ( 35 ) . with the increase of such peptides annually , it was realized in the 1990s that a database would be useful to help manage the basic information for amps . to our knowledge , alex tossi et  al . built the first such database for plant and animal amps in 1998 ( 13 ) . , both the apd and antimic were published . in 2012 , antimic with 1700 entries ( 14 ) was replaced by dampd with a reduced number of 1232 entries ( 15 ) . the 2004 version of the antimicrobial peptide database ( apd ) with 525 amps ( 16 ) was widely accepted and utilized . in 2009 , it was updated to the apd2 with 1228 entries ( 17 ) . since the publication of the apd2 , the database web hits increased exponentially ( over 1 million in 2014 ) . one of the most important reasons for this could be that the apd registers amps with a set of defined criteria and is regularly updated by an investigator in the amp field . in addition , each entry is highly integrated with additional peptide information covering various aspects of amps . to help users better use this resource , here we summarize the main features of this updated database , which we refer to as the apd3 . we also highlight multiple applications of this database in both research and education . to generate a clean data set , this database currently focuses on ( i ) natural amps with ( ii ) a known amino acid sequence , ( iii ) biological activity and ( iv ) a size less than 100 residues . more recently , the polypeptide size was further relaxed to 200 residues so that important human antimicrobial proteins can be included . a unique and powerful feature of the apd3 is that its search interface consists of a pipeline of search functions . the more one selects or enters , the less one will get . without activating anything in the interface , a simple search returns all the peptides in the database ( current total 2619 ) . the users can filter the information freely at their will . to make it more convenient , the apd3 has enhanced the search interface by re - grouping the existing search icons into functional zones based on information types and by adding new search icons for peptide activity . at the bottom of the search page , users can sort the information based on peptide apd i d ( default ) , net charge , length and hydrophobic content . in the following , we briefly describe the main features of the current apd3 , ranging from peptide search , prediction , statistics and educational web pages to additional tools . the apd3 database has classified the sources of the natural peptides based on the six life kingdoms and the three life domains ( 28,29 ) . the six life domains ( count of amps ) adopted by the apd3 are bacteria ( 261 bacteriocins ) , archaea ( 4 peptides ) , protists ( 7 entries ) , fungi ( 13 peptides ) , plants ( 321 entries ) and animals ( 1973 amps ) . thus , the majority of amps ( 75% ) originate from animals , especially amphibians , which account for 38% . based on the above data , there are 261 bacteriocins from bacteria , 4 peptides from archaea and 2314 host defense peptides from eukaryota . animals. in the same manner , one can also search amps from amphibians , fish , reptiles , birds , insects , spiders , scorpions , molluscs , crustaceans and chelicerata ( amp counts listed on the apd3 main page ) . also searchable are peptide families ( defensins , cathelicidins , histatins , maximins , aureins , brevinins , dermaseptins , esculentins , temporins , cyclotides , lantibiotics , pro - rich or trp - rich peptides , to list just a few ) . in addition , one can obtain a list of validated amps for any organism using scientific names . for example , a search of homo sapiens in the field of  source organism led to 112 human amps.peptide sequence search . sequence search ( using single letter codes ) is the most accurate method to find out whether a peptide has been registered in the apd3 . for example , 1440 amps contain at least one cysteine . to reduce sequence redundancy , amps from different species that share the same sequence occupy a single entry in the database . such peptides ( currently 55 ) can be searched in the  additional information by using  found in multiple species. in addition , synthetic peptide fragments of natural amps are treated as derivatives and can be listed in the same entry.chemical modifications . since 2009 ( 17 ) , the apd3 has annotated 24 types of chemical modifications for amps . these modifications can be searched in the  name field using the xx search keys in table 1 . table 1.search keys for 24 types of post - translational modifications of ampskeymodificationkeymodificationkeymodificationxxaamidationxxjsidechain - backbone cyclizationxxrreductionxxbchromophore / ion - binding moietiesxxkhydroxylationxxssulfationxxcbackbone cyclizationxxllipidationxxtthioether bridgexxdd - amino acidsxxmmethylationxxurana box via a single s - s bondxxeacetylationxxnnitrolationxxvlantibiotic c - c bridgexxfcarboxylic - acid - containing unitxxooxidationxxwdehydrationxxgglycosylationxxpphosphorylationxxxadp - ribosylationxxhhalogenation ( cl , br)xxqn - terminal cyclic glutamatexxycitrullinationsearch in the  name field of the apd3 by entering the keys such as xxa.peptide parameters . in this zone note that the net charge in the apd3 differs from other databases due to the consideration of the effect of chemical modifications . for instance , the net charge ( ph 7 ) of all peptides with c - terminal amidation is increased by + 1 in the apd3 compared to those in other databases ( 1827).structure classifications . three - dimensional structural information has been annotated in the apd since 2003 ( 16 ) . if the coordinates of a peptide are deposited , users can rotate and view the 3d structure in the pdb directly via the apd3 link . the link usually points at the structure solved at the highest resolution when there are multiple coordinates from different crystals or determined by different methods such as x - ray diffraction ( 44 structures ) or nmr spectroscopy ( 307 structures ) . once in the pdb ( 30 ) , users can also view other related structures and properties of the same peptide . version 3 also annotated 155 structures suggested by circular dichroism ( cd ) , which provides clear evidence for helical structures . although there are different schemes in the literature for structural classification ( 16 ) , the apd3 has adopted a unified classification proposed by wang ( 9 ) . the four peptide classes are  ,  ,  and non-. currently , the  family contains 362 amps with known -helical structures . the  family is composed of 98 peptides with a -sheet structure . while the  family holds 98 amps with both  and  structures , 9 peptides in the non- family have neither  nor  structures . structure. because not all peptides have known 3d structures , the apd3 has also adopted a universal classification system based on the covalent bonding patterns of polypeptide chains ( 31 ) . in this unified classification , the first class ( ucll ) includes all linear peptides where chemical modifications occur only within the same amino acid . the second class ( ucss ) is made of all peptides with at least one chemical bond between the side chains of different amino acids of the polypeptide . the third class ( ucsb ) contains all peptides with a chemical bond between the side chain of residue i and the backbone of residue j ( i  j ) . finally , the fourth class ( ucbb ) comprises all peptides with a circular backbone ( i.e. a covalent bond is formed between the n and c - termini of the polypeptide ) . further details for this unified peptide classification method can be found elsewhere ( 31).beyond antimicrobials . it is established that the functions of amps are not limited to antimicrobial ( 19 ) . the apd has been continuously annotating new peptide functions such as antioxidant , wound healing and toxin neutralization . the expansion of the peptide function zone in different versions of the apd is summarized in table 2 . it is evident that the apd3 contains 10 more searchable peptide activities , leading to a total of 19 , which can be viewed via the main page ( http://aps.unmc.edu/ap ) or searched from the search interface of the apd3 . table 2.expansion of searchable peptide functions in the antimicrobial peptide databasefunctionapdapd2apd3countantibacterial2169antiviral172antifungal961anticancer185hemolytic307anti - hiv105anti - gram+426anti - gram-202toxin neutralizing ( e.g. lps / endotoxin)61antiparasitic80antimalarial16spermicidal11insecticidal27anti - protist4chemotactic53wound healing10antioxidant19protease inhibitor12antibiofilm16target organisms , mechanisms of action and animal models . in the additional information zone this information can be searched by entering abbreviated microbe names such as e. coli , s. aureus and c. albicans ( one at a time ) . thus , users can obtain a set of amps that are known to have an antimicrobial effect on any pathogen of interest as long as they have been determined and registered into the database . the mechanism of action , when known , is also described in the additional information field . one can use the bb keys ( table 3 ) to search for such information ( 17 ) . for example , we obtained 24 peptides that bind to lipid ii to inhibit cell wall synthesis by entering bbw into the  name field . in the additional information field , the apd3 also started to annotate animal models used to test the peptide efficacy in vivo . at present , a search of , users can refer to the original articles using the links provided by the apd3 . table 3.binding partners of antimicrobial peptidessearch keyamp partnertarget sitecurrent countbbbh2ooligomers in waterin solution15bbiimetals ( e.g. zn , ca)in solution16bbscarbohydratesfungal surface49bbwlipid iigram+ bacterial cell wall24bbllps ( endotoxin)gram- bacteria outer membranes61bbrsurface receptorscell surface4bbmmbacterial membranes(inner ) membranes93bbbmoligomers in membranesmembranes4bbnnucleic acidswithin the cells ; nets outside the cells15bbriboribosomeswithin bacteria2searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs).the year of amp discovery and author search . the apd3 also enabled a search of amps based on the year of discovery or an author . based on this , we found 100 new natural amps per year since 2000 ( 32 ) . michael conlon ( 33 ) is one of the most productive contributors since his name is linked to 309 entries in this database.the updated prediction interface . it now predicts the possibility of a sequence to be amps based on the entire parameter space defined by all the natural peptides registered in the database . this objective justifies our focus on natural amps with demonstrated activity so that this parameter space is not distorted by synthetic peptides or predicted sequences.statistical information . the structural statistics has been mentioned above , while the amp function statistics is summarized in table 2 . for updated statistics , , we created a web page my tools , which provides 16 links to various online programs for helical wheel projection , as well as predictions of signal sequence in a pro - peptide , peptide half - life , instability index , alpha index , cell penetrating ability , antigenicity and 3d structure.web pages for education . nomenclature lists four typical methods for amp naming , while classification provides seven major methods for amp classification . the 3d structure describes structure annotation , determination methods , classification , viewing , structure citation and statistics . glossary provides definitions for commonly used amp terms and abbreviations , including the bb and xx keys created for the apd3 search . because many users requested sequence downloads , this has been provided on the main page of the apd3 . finally , the apd3 updates the users with new database additions via the what 's new web page . source organism classification and search . the apd3 database has classified the sources of the natural peptides based on the six life kingdoms and the three life domains ( 28,29 ) . the six life domains ( count of amps ) adopted by the apd3 are bacteria ( 261 bacteriocins ) , archaea ( 4 peptides ) , protists ( 7 entries ) , fungi ( 13 peptides ) , plants ( 321 entries ) and animals ( 1973 amps ) . thus , the majority of amps ( 75% ) originate from animals , especially amphibians , which account for 38% . based on the above data there are 261 bacteriocins from bacteria , 4 peptides from archaea and 2314 host defense peptides from eukaryota . animals. in the same manner , one can also search amps from amphibians , fish , reptiles , birds , insects , spiders , scorpions , molluscs , crustaceans and chelicerata ( amp counts listed on the apd3 main page ) . also searchable are peptide families ( defensins , cathelicidins , histatins , maximins , aureins , brevinins , dermaseptins , esculentins , temporins , cyclotides , lantibiotics , pro - rich or trp - rich peptides , to list just a few ) . in addition , one can obtain a list of validated amps for any organism using scientific names . for example , a search of homo sapiens in the field of  source organism led to 112 human amps . peptide sequence search . sequence search ( using single letter codes ) is the most accurate method to find out whether a peptide has been registered in the apd3 . for example , 1440 amps contain at least one cysteine . to reduce sequence redundancy , amps from different species that share the same sequence occupy a single entry in the database . such peptides ( currently 55 ) can be searched in the  additional information by using  found in multiple species. in addition , synthetic peptide fragments of natural amps are treated as derivatives and can be listed in the same entry . chemical modifications . since 2009 ( 17 ) , the apd3 has annotated 24 types of chemical modifications for amps . these modifications can be searched in the  name field using the xx search keys in table 1 . table 1.search keys for 24 types of post - translational modifications of ampskeymodificationkeymodificationkeymodificationxxaamidationxxjsidechain - backbone cyclizationxxrreductionxxbchromophore / ion - binding moietiesxxkhydroxylationxxssulfationxxcbackbone cyclizationxxllipidationxxtthioether bridgexxdd - amino acidsxxmmethylationxxurana box via a single s - s bondxxeacetylationxxnnitrolationxxvlantibiotic c - c bridgexxfcarboxylic - acid - containing unitxxooxidationxxwdehydrationxxgglycosylationxxpphosphorylationxxxadp - ribosylationxxhhalogenation ( cl , br)xxqn - terminal cyclic glutamatexxycitrullinationsearch in the  name field of the apd3 by entering the keys such as xxa . search in the  name field of the apd3 by entering the keys such as xxa . peptide parameters . in this zone , one can search peptide length , net charge and hydrophobic content . note that the net charge in the apd3 differs from other databases due to the consideration of the effect of chemical modifications . for instance , the net charge ( ph 7 ) of all peptides with c - terminal amidation is increased by + 1 in the apd3 compared to those in other databases ( 1827 ) . structure classifications . three - dimensional structural information has been annotated in the apd since 2003 ( 16 ) . if the coordinates of a peptide are deposited , users can rotate and view the 3d structure in the pdb directly via the apd3 link . the link usually points at the structure solved at the highest resolution when there are multiple coordinates from different crystals or determined by different methods such as x - ray diffraction ( 44 structures ) or nmr spectroscopy ( 307 structures ) . once in the pdb ( 30 ) , users can also view other related structures and properties of the same peptide . version 3 also annotated 155 structures suggested by circular dichroism ( cd ) , which provides clear evidence for helical structures . although there are different schemes in the literature for structural classification ( 16 ) , the apd3 has adopted a unified classification proposed by wang ( 9 ) . the four peptide classes are  ,  ,  and non-. currently , the  family contains 362 amps with known -helical structures . the  family is composed of 98 peptides with a -sheet structure . while the  family holds 98 amps with both  and  structures , 9 peptides in the non- family have neither  nor  structures . structure. because not all peptides have known 3d structures , the apd3 has also adopted a universal classification system based on the covalent bonding patterns of polypeptide chains ( 31 ) . in this unified classification , the first class ( ucll ) includes all linear peptides where chemical modifications occur only within the same amino acid . the second class ( ucss ) is made of all peptides with at least one chemical bond between the side chains of different amino acids of the polypeptide . the third class ( ucsb ) contains all peptides with a chemical bond between the side chain of residue i and the backbone of residue j ( i  j ) . finally , the fourth class ( ucbb ) comprises all peptides with a circular backbone ( i.e. a covalent bond is formed between the n and c - termini of the polypeptide ) . further details for this unified peptide classification method can be found elsewhere ( 31 ) . beyond antimicrobials . it is established that the functions of amps are not limited to antimicrobial ( 19 ) . the apd has been continuously annotating new peptide functions such as antioxidant , wound healing and toxin neutralization . the expansion of the peptide function zone in different versions of the apd is summarized in table 2 . it is evident that the apd3 contains 10 more searchable peptide activities , leading to a total of 19 , which can be viewed via the main page ( http://aps.unmc.edu/ap ) or searched from the search interface of the apd3 . table 2.expansion of searchable peptide functions in the antimicrobial peptide databasefunctionapdapd2apd3countantibacterial2169antiviral172antifungal961anticancer185hemolytic307anti - hiv105anti - gram+426anti - gram-202toxin neutralizing ( e.g. lps / endotoxin)61antiparasitic80antimalarial16spermicidal11insecticidal27anti - protist4chemotactic53wound healing10antioxidant19protease inhibitor12antibiofilm16 target organisms , mechanisms of action and animal models . in the additional information zone this information can be searched by entering abbreviated microbe names such as e. coli , s. aureus and c. albicans ( one at a time ) . thus , users can obtain a set of amps that are known to have an antimicrobial effect on any pathogen of interest as long as they have been determined and registered into the database . the mechanism of action , when known , is also described in the additional information field . one can use the bb keys ( table 3 ) to search for such information ( 17 ) . for example , we obtained 24 peptides that bind to lipid ii to inhibit cell wall synthesis by entering bbw into the  name field . in the additional information field , the apd3 also started to annotate animal models used to test the peptide efficacy in vivo . at present , a search of , users can refer to the original articles using the links provided by the apd3 . table 3.binding partners of antimicrobial peptidessearch keyamp partnertarget sitecurrent countbbbh2ooligomers in waterin solution15bbiimetals ( e.g. zn , ca)in solution16bbscarbohydratesfungal surface49bbwlipid iigram+ bacterial cell wall24bbllps ( endotoxin)gram- bacteria outer membranes61bbrsurface receptorscell surface4bbmmbacterial membranes(inner ) membranes93bbbmoligomers in membranesmembranes4bbnnucleic acidswithin the cells ; nets outside the cells15bbriboribosomeswithin bacteria2searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs ) . searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs ) . the apd3 also enabled a search of amps based on the year of discovery or an author . based on this , we found 100 new natural amps per year since 2000 ( 32 ) . michael conlon ( 33 ) is one of the most productive contributors since his name is linked to 309 entries in this database . the updated prediction interface . it now predicts the possibility of a sequence to be amps based on the entire parameter space defined by all the natural peptides registered in the database . this objective justifies our focus on natural amps with demonstrated activity so that this parameter space is not distorted by synthetic peptides or predicted sequences . statistical information . the structural statistics has been mentioned above , while the amp function statistics is summarized in table 2 . for updated statistics , to further expand the capability of the apd3 , we created a web page my tools , which provides 16 links to various online programs for helical wheel projection , as well as predictions of signal sequence in a pro - peptide , peptide half - life , instability index , alpha index , cell penetrating ability , antigenicity and 3d structure . nomenclature lists four typical methods for amp naming , while classification provides seven major methods for amp classification . the 3d structure describes structure annotation , determination methods , classification , viewing , structure citation and statistics . glossary provides definitions for commonly used amp terms and abbreviations , including the bb and xx keys created for the apd3 search . because many users requested sequence downloads , this has been provided on the main page of the apd3 . finally , the apd3 updates the users with new database additions via the what 's new web page . to generate a clean data set , the apd3 has set up criteria for peptide registration . this database currently focuses on ( i ) natural amps with ( ii ) a known amino acid sequence , ( iii ) biological activity and ( iv ) a size less than 100 residues . more recently , the polypeptide size was further relaxed to 200 residues so that important human antimicrobial proteins can be included . a unique and powerful feature of the apd3 is that its search interface consists of a pipeline of search functions . the more one selects or enters , the less one will get . without activating anything in the interface , a simple search returns all the peptides in the database ( current total 2619 ) . the users can filter the information freely at their will . to make it more convenient , the apd3 has enhanced the search interface by re - grouping the existing search icons into functional zones based on information types and by adding new search icons for peptide activity . at the bottom of the search page , users can sort the information based on peptide apd i d ( default ) , net charge , length and hydrophobic content . in the following , we briefly describe the main features of the current apd3 , ranging from peptide search , prediction , statistics and educational web pages to additional tools . 
 source organism classification and search . the apd3 database has classified the sources of the natural peptides based on the six life kingdoms and the three life domains ( 28,29 ) . the six life domains ( count of amps ) adopted by the apd3 are bacteria ( 261 bacteriocins ) , archaea ( 4 peptides ) , protists ( 7 entries ) , fungi ( 13 peptides ) , plants ( 321 entries ) and animals ( 1973 amps ) . thus , the majority of amps ( 75% ) originate from animals , especially amphibians , which account for 38% . based on the above data there are 261 bacteriocins from bacteria , 4 peptides from archaea and 2314 host defense peptides from eukaryota . animals. in the same manner , one can also search amps from amphibians , fish , reptiles , birds , insects , spiders , scorpions , molluscs , crustaceans and chelicerata ( amp counts listed on the apd3 main page ) . also searchable are peptide families ( defensins , cathelicidins , histatins , maximins , aureins , brevinins , dermaseptins , esculentins , temporins , cyclotides , lantibiotics , pro - rich or trp - rich peptides , to list just a few ) . in addition , one can obtain a list of validated amps for any organism using scientific names . for example , a search of homo sapiens in the field of  source organism led to 112 human amps.peptide sequence search . sequence search ( using single letter codes ) is the most accurate method to find out whether a peptide has been registered in the apd3 . for example , 1440 amps contain at least one cysteine . to reduce sequence redundancy , amps from different species that share the same sequence occupy a single entry in the database synthetic peptide fragments of natural amps are treated as derivatives and can be listed in the same entry.chemical modifications . since 2009 ( 17 ) , the apd3 has annotated 24 types of chemical modifications for amps . these modifications can be searched in the  name field using the xx search keys in table 1 . table 1.search keys for 24 types of post - translational modifications of ampskeymodificationkeymodificationkeymodificationxxaamidationxxjsidechain - backbone cyclizationxxrreductionxxbchromophore / ion - binding moietiesxxkhydroxylationxxssulfationxxcbackbone cyclizationxxllipidationxxtthioether bridgexxdd - amino acidsxxmmethylationxxurana box via a single s - s bondxxeacetylationxxnnitrolationxxvlantibiotic c - c bridgexxfcarboxylic - acid - containing unitxxooxidationxxwdehydrationxxgglycosylationxxpphosphorylationxxxadp - ribosylationxxhhalogenation ( cl , br)xxqn - terminal cyclic glutamatexxycitrullinationsearch in the  name field of the apd3 by entering the keys such as xxa.peptide parameters . in this zone note that the net charge in the apd3 differs from other databases due to the consideration of the effect of chemical modifications . for instance , the net charge ( ph 7 ) of all peptides with c - terminal amidation is increased by + 1 in the apd3 compared to those in other databases ( 1827).structure classifications . three - dimensional structural information has been annotated in the apd since 2003 ( 16 ) . if the coordinates of a peptide are deposited , users can rotate and view the 3d structure in the pdb directly via the apd3 link . the link usually points at the structure solved at the highest resolution when there are multiple coordinates from different crystals or determined by different methods such as x - ray diffraction ( 44 structures ) or nmr spectroscopy ( 307 structures ) . once in the pdb ( 30 ) , users can also view other related structures and properties of the same peptide . version 3 also annotated 155 structures suggested by circular dichroism ( cd ) , which provides clear evidence for helical structures . although there are different schemes in the literature for structural classification ( 16 ) , the apd3 has adopted a unified classification proposed by wang ( 9 ) . the four peptide classes are  ,  ,  and non-. currently , the  family contains 362 amps with known -helical structures . while the  family holds 98 amps with both  and  structures , 9 peptides in the non- family have neither  nor  structures . such peptide counts can be obtained from the search interface under structure. because not all peptides have known 3d structures , the apd3 has also adopted a universal classification system based on the covalent bonding patterns of polypeptide chains ( 31 ) . in this unified classification , the first class ( ucll ) includes all linear peptides where chemical modifications occur only within the same amino acid . the second class ( ucss ) is made of all peptides with at least one chemical bond between the side chains of different amino acids of the polypeptide . the third class ( ucsb ) contains all peptides with a chemical bond between the side chain of residue i and the backbone of residue j ( i  j ) . finally , the fourth class ( ucbb ) comprises all peptides with a circular backbone ( i.e. a covalent bond is formed between the n and c - termini of the polypeptide ) . further details for this unified peptide classification method can be found elsewhere ( 31).beyond antimicrobials . it is established that the functions of amps are not limited to antimicrobial ( 19 ) . the apd has been continuously annotating new peptide functions such as antioxidant , wound healing and toxin neutralization . the expansion of the peptide function zone in different versions of the apd is summarized in table 2 . it is evident that the apd3 contains 10 more searchable peptide activities , leading to a total of 19 , which can be viewed via the main page ( http://aps.unmc.edu/ap ) or searched from the search interface of the apd3 . table 2.expansion of searchable peptide functions in the antimicrobial peptide databasefunctionapdapd2apd3countantibacterial2169antiviral172antifungal961anticancer185hemolytic307anti - hiv105anti - gram+426anti - gram-202toxin neutralizing ( e.g. lps / endotoxin)61antiparasitic80antimalarial16spermicidal11insecticidal27anti - protist4chemotactic53wound healing10antioxidant19protease inhibitor12antibiofilm16target organisms , mechanisms of action and animal models . in the additional information zone this information can be searched by entering abbreviated microbe names such as e. coli , s. aureus and c. albicans ( one at a time ) . thus , users can obtain a set of amps that are known to have an antimicrobial effect on any pathogen of interest as long as they have been determined and registered into the database . the mechanism of action , when known , is also described in the additional information field . one can use the bb keys ( table 3 ) to search for such information ( 17 ) . for example , we obtained 24 peptides that bind to lipid ii to inhibit cell wall synthesis by entering bbw into the  name field . in the additional information field , the apd3 also started to annotate animal models used to test the peptide efficacy in vivo . at present , a search of , users can refer to the original articles using the links provided by the apd3 . table 3.binding partners of antimicrobial peptidessearch keyamp partnertarget sitecurrent countbbbh2ooligomers in waterin solution15bbiimetals ( e.g. zn , ca)in solution16bbscarbohydratesfungal surface49bbwlipid iigram+ bacterial cell wall24bbllps ( endotoxin)gram- bacteria outer membranes61bbrsurface receptorscell surface4bbmmbacterial membranes(inner ) membranes93bbbmoligomers in membranesmembranes4bbnnucleic acidswithin the cells ; nets outside the cells15bbriboribosomeswithin bacteria2searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs).the year of amp discovery and author search . the apd3 also enabled a search of amps based on the year of discovery or an author . based on this , we found 100 new natural amps per year since 2000 ( 32 ) . michael conlon ( 33 ) is one of the most productive contributors since his name is linked to 309 entries in this database.the updated prediction interface . it now predicts the possibility of a sequence to be amps based on the entire parameter space defined by all the natural peptides registered in the database . this objective justifies our focus on natural amps with demonstrated activity so that this parameter space is not distorted by synthetic peptides or predicted sequences.statistical information . the structural statistics has been mentioned above , while the amp function statistics is summarized in table 2 . for updated statistics , , we created a web page my tools , which provides 16 links to various online programs for helical wheel projection , as well as predictions of signal sequence in a pro - peptide , peptide half - life , instability index , alpha index , cell penetrating ability , antigenicity and 3d structure.web pages for education . nomenclature lists four typical methods for amp naming , while classification provides seven major methods for amp classification . the 3d structure describes structure annotation , determination methods , classification , viewing , structure citation and statistics . glossary provides definitions for commonly used amp terms and abbreviations , including the bb and xx keys created for the apd3 search . because many users requested sequence downloads , this has been provided on the main page of the apd3 . finally , the apd3 updates the users with new database additions via the what 's new web page . source organism classification and search . the apd3 database has classified the sources of the natural peptides based on the six life kingdoms and the three life domains ( 28,29 ) . the six life domains ( count of amps ) adopted by the apd3 are bacteria ( 261 bacteriocins ) , archaea ( 4 peptides ) , protists ( 7 entries ) , fungi ( 13 peptides ) , plants ( 321 entries ) and animals ( 1973 amps ) . thus , the majority of amps ( 75% ) originate from animals , especially amphibians , which account for 38% . based on the above data there are 261 bacteriocins from bacteria , 4 peptides from archaea and 2314 host defense peptides from eukaryota . animals. in the same manner , one can also search amps from amphibians , fish , reptiles , birds , insects , spiders , scorpions , molluscs , crustaceans and chelicerata ( amp counts listed on the apd3 main page ) . also searchable are peptide families ( defensins , cathelicidins , histatins , maximins , aureins , brevinins , dermaseptins , esculentins , temporins , cyclotides , lantibiotics , pro - rich or trp - rich peptides , to list just a few ) . in addition , one can obtain a list of validated amps for any organism using scientific names . for example , a search of homo sapiens in the field of  source organism led to 112 human amps . peptide sequence search . sequence search ( using single letter codes ) is the most accurate method to find out whether a peptide has been registered in the apd3 . for example , 1440 amps contain at least one cysteine . to reduce sequence redundancy , amps from different species that share the same sequence occupy a single entry in the database synthetic peptide fragments of natural amps are treated as derivatives and can be listed in the same entry . chemical modifications . since 2009 ( 17 ) , the apd3 has annotated 24 types of chemical modifications for amps . these modifications can be searched in the  name field using the xx search keys in table 1 . table 1.search keys for 24 types of post - translational modifications of ampskeymodificationkeymodificationkeymodificationxxaamidationxxjsidechain - backbone cyclizationxxrreductionxxbchromophore / ion - binding moietiesxxkhydroxylationxxssulfationxxcbackbone cyclizationxxllipidationxxtthioether bridgexxdd - amino acidsxxmmethylationxxurana box via a single s - s bondxxeacetylationxxnnitrolationxxvlantibiotic c - c bridgexxfcarboxylic - acid - containing unitxxooxidationxxwdehydrationxxgglycosylationxxpphosphorylationxxxadp - ribosylationxxhhalogenation ( cl , br)xxqn - terminal cyclic glutamatexxycitrullinationsearch in the  name field of the apd3 by entering the keys such as xxa . search in the  name field of the apd3 by entering the keys such as xxa . note that the net charge in the apd3 differs from other databases due to the consideration of the effect of chemical modifications . for instance , the net charge ( ph 7 ) of all peptides with c - terminal amidation is increased by + 1 in the apd3 compared to those in other databases ( 1827 ) . structure classifications . three - dimensional structural information has been annotated in the apd since 2003 ( 16 ) . if the coordinates of a peptide are deposited , users can rotate and view the 3d structure in the pdb directly via the apd3 link . the link usually points at the structure solved at the highest resolution when there are multiple coordinates from different crystals or determined by different methods such as x - ray diffraction ( 44 structures ) or nmr spectroscopy ( 307 structures ) . once in the pdb ( 30 ) , users can also view other related structures and properties of the same peptide . version 3 also annotated 155 structures suggested by circular dichroism ( cd ) , which provides clear evidence for helical structures . although there are different schemes in the literature for structural classification ( 16 ) , the apd3 has adopted a unified classification proposed by wang ( 9 ) . the four peptide classes are  ,  ,  and non-. currently , the  family contains 362 amps with known -helical structures . the  family is composed of 98 peptides with a -sheet structure . while the  family holds 98 amps with both  and  structures , 9 peptides in the non- family have neither  nor  structures . structure. because not all peptides have known 3d structures , the apd3 has also adopted a universal classification system based on the covalent bonding patterns of polypeptide chains ( 31 ) . in this unified classification , the first class ( ucll ) includes all linear peptides where chemical modifications occur only within the same amino acid . the second class ( ucss ) is made of all peptides with at least one chemical bond between the side chains of different amino acids of the polypeptide . the third class ( ucsb ) contains all peptides with a chemical bond between the side chain of residue i and the backbone of residue j ( i  j ) . finally , the fourth class ( ucbb ) comprises all peptides with a circular backbone ( i.e. a covalent bond is formed between the n and c - termini of the polypeptide ) . further details for this unified peptide classification method can be found elsewhere ( 31 ) . beyond antimicrobials . it is established that the functions of amps are not limited to antimicrobial ( 19 ) . the apd has been continuously annotating new peptide functions such as antioxidant , wound healing and toxin neutralization . the expansion of the peptide function zone in different versions of the apd is summarized in table 2 . it is evident that the apd3 contains 10 more searchable peptide activities , leading to a total of 19 , which can be viewed via the main page ( http://aps.unmc.edu/ap ) or searched from the search interface of the apd3 . table 2.expansion of searchable peptide functions in the antimicrobial peptide databasefunctionapdapd2apd3countantibacterial2169antiviral172antifungal961anticancer185hemolytic307anti - hiv105anti - gram+426anti - gram-202toxin neutralizing ( e.g. lps / endotoxin)61antiparasitic80antimalarial16spermicidal11insecticidal27anti - protist4chemotactic53wound healing10antioxidant19protease inhibitor12antibiofilm16 target organisms , mechanisms of action and animal models . in the additional information zone this information can be searched by entering abbreviated microbe names such as e. coli , s. aureus and c. albicans ( one at a time ) . thus , users can obtain a set of amps that are known to have an antimicrobial effect on any pathogen of interest as long as they have been determined and registered into the database . the mechanism of action , when known , is also described in the additional information field . one can use the bb keys ( table 3 ) to search for such information ( 17 ) . for example , we obtained 24 peptides that bind to lipid ii to inhibit cell wall synthesis by entering bbw into the  name field . in the additional information field , the apd3 also started to annotate animal models used to test the peptide efficacy in vivo . at present , a search of , users can refer to the original articles using the links provided by the apd3 . table 3.binding partners of antimicrobial peptidessearch keyamp partnertarget sitecurrent countbbbh2ooligomers in waterin solution15bbiimetals ( e.g. zn , ca)in solution16bbscarbohydratesfungal surface49bbwlipid iigram+ bacterial cell wall24bbllps ( endotoxin)gram- bacteria outer membranes61bbrsurface receptorscell surface4bbmmbacterial membranes(inner ) membranes93bbbmoligomers in membranesmembranes4bbnnucleic acidswithin the cells ; nets outside the cells15bbriboribosomeswithin bacteria2searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs ) . searched in the  name field of the apd3 ( http://aps.unmc.edu/ap ) in october 2015 using the keys ( e.g. bbs ) . the apd3 also enabled a search of amps based on the year of discovery or an author . based on this , we found 100 new natural amps per year since 2000 ( 32 ) . michael conlon ( 33 ) is one of the most productive contributors since his name is linked to 309 entries in this database . the updated prediction interface . it now predicts the possibility of a sequence to be amps based on the entire parameter space defined by all the natural peptides registered in the database . this objective justifies our focus on natural amps with demonstrated activity so that this parameter space is not distorted by synthetic peptides or predicted sequences . statistical information . the structural statistics has been mentioned above , while the amp function statistics is summarized in table 2 . for updated statistics , to further expand the capability of the apd3 , we created a web page my tools , which provides 16 links to various online programs for helical wheel projection , as well as predictions of signal sequence in a pro - peptide , peptide half - life , instability index , alpha index , cell penetrating ability , antigenicity and 3d structure . nomenclature lists four typical methods for amp naming , while classification provides seven major methods for amp classification . the 3d structure describes structure annotation , determination methods , classification , viewing , structure citation and statistics . glossary provides definitions for commonly used amp terms and abbreviations , including the bb and xx keys created for the apd3 search . because many users requested sequence downloads , this has been provided on the main page of the apd3 . finally , the apd3 updates the users with new database additions via the what 's new web page . it is now recognized that the amino acid composition of amps is one of the most important parameters for peptide classification , prediction and design ( 9,31 ) . to our knowledge , the apd is the first database that provides a program for calculations of the amino acid composition for amps from a variety of families ( 16 ) . a plot of the amino acid occurring frequency versus the 20 amino acids for a family of peptides generates the amino acid profile or signature . select amino acid profiles for amps from different life groups ( e.g. bacteria , plants , amphibians , birds , reptiles , fish and humans ) , activity groups ( such as antibacterial , antiviral , antifungal and anticancer ) and structure groups (  ,  ,  and non- ) , have been presented elsewhere ( 34 ) . here we present the amino acid profiles for the four unified peptide classes ( 31 ) based on the data already annotated in the apd3 ( figure 1 ) . the 694 linear amps ( ucll ) are abundant ( 10% ) in amino acids l , a , g and k. to view the differences between lantibiotics and defensins , we split the sidechain - connected ucss class into ucss1a and ucss1b . while the disulfide - bond linked amps ( ucss1a ) are abundant in c , g and k , the ucss1b subclass ( mainly lantibiotics ) is abundant in c , t and s , which form multiple thioether bonds . as described elsewhere ( 31 ) , the ucss1a class can also be further divided into subclasses . the 306 defensins with a -sheet structure are abundant in c , g and r. cysteines and glycines are important structural residues , whereas arginines confer biological functions ( 9 ) . in the ucss1a class , the abundant residues are l and k in the helical subclass containing three disulfide bonds . the abundant residues ( l , a , g and k ) of this subclass are identical to those of all amphibian amps ( 1007 entries ) or a subset of 117 frog amps with a known helical structure . interestingly , the third class ucsb , with a chemical bond between the side chain and peptide backbone ( 22 members ) , is abundant in v , a and g. finally , the 189 circular amps in the ucbb class ( with a peptide bond between the n and c termini ) are abundant in c and g only . it is clear that the amino acid profile or signature depends on the peptide class ( figure 1 ) . amino acid profiles of the four universal classes of amps ( 31 ) . for further details , see the text . the data size , length and averaged net charge for the peptide classes can be found in table 4 . in addition , these unified classes of amps in the apd3 also vary in average peptide length and net charge ( table 4 ) . while the average net charge is in the following order : ucss1a > ucll > ucss1b > ucbb > ucsb , the order for the average peptide length is ucss1a > ucbb > ucss1b > ucll > ucsb . it is interesting that the disulfide bond - linked amps ( ucss1a ) , most positive in net charge , are also longest on average . in contrast , the amps generated via a sidechain - backbone connection ( i.e. the ucsb class ) are not only shortest in length but also lowest in net charge ( table 4 ) . such derived net charges , lengths and abundant amino acids ( figure 1 and table 4 ) can be useful for predicting or designing amps from different classes . for instance , entering ucll into the  name field followed by search returned 694 peptides . the highest and lowest average lengths and net charges are in bold since its publication in nucleic acids research in 2004 ( 16 ) , the apd has been utilized for a variety of purposes . in the following , users can search peptide sequence , source , activity , structure , chemical modification , peptide properties ( such as net charge , length , hydrophobic% , binding partners ) , the year of publication , author , mechanism of action and more.peptide property calculations . in addition to peptide length , net charge , amino acid composition and boman index previously programmed in the apd ( 16 ) , the apd3 enabled the calculations of molecular weight , molecular formula , molar extinction coefficient and gravy ( 35).peptide classification method development . as described above , the apd also enabled us to propose unified classification schemes for 3d structures as well as sequences of amps ( 9,31).identification of the most similar sequences . once a new peptide is sequenced , one would like to know which known sequences it most resembles . ( 36 ) found no homologous sequences for bactofencin a using the blast database , but identified similar sequences in the apd2.amp statistics . the apd3 provides an average net charge of + 3.2 and length of 32.7 based on the 2619 amps . these statistical parameters are useful for describing the general properties of amps ( see also figure 1 and table 4).cleavage sequence selection for recombinant amp expression . in the apd3 , there were 754 amps containing a methionine residue ( m ) and only 76 peptides containing a dp pair . such a dramatic difference formed the basis for our previous creation of a dp sequence as a cleavage site to release the recombinant form of human cathelicidin ll-37 from the expressed fusion protein by formic acid ( 37 ) . because less amps contain the dp site than m , this cleavage site can have a broader application in expression and purification of amps with a native sequence ( 38).template selection for structure - activity relationship ( sar ) studies . to understand why a bacterial membrane anchor is not toxic , we used the apd to identify aurein 1.2 that shares the n - terminal glfd sequence with the membrane anchor ( 39 ) . this study revealed the importance of peptide length or hydrophobicity for peptide activity.peptide property improvements . based on the arginine / lysine ratio in amps with different activities , the antiviral peptides were found to have the highest arginine content compared to other activity groups . this finding enabled us to improve anti - hiv activity of known amps by introducing additional arginines ( 40).peptide design . based on the 525 entries in the apd ( 16 ) , loose developed the grammar approach ( 41 ) . using the apd2 , we developed a database filtering technology for peptide design ( 42 ) . by combining the most probable parameters derived from the database , we were able to obtain a potent peptide against methicillin - resistant s. aureus ( mrsa ) . since the abundant amino acids in the apd2 are glycines , lysines and leucines ( 17 ) , gellman ( 43 ) introduced a glycine - like unit into synthetic polymers , leading to improved cell selectivity ( i.e. more toxic against bacteria and less toxic to human cells).construction of new prediction programs . lata et al . ( 44 ) first used the apd sequences as a positive training set to program machine - learning algorithms for amp prediction . ( 45 ) tested a two - level multi - label classifier iamp-2l based on the multiple functions of amps annotated in the apd2 . found that the apd2 was able to predict more possible amps than existing machine - learning programs online ( 46 ) . as a new addition to the apd3 , users can access select peptide prediction programs directly from the apd links.construction of new databases . since the apd is an open resource , it allowed others to copy this database to build other databases such as camp , lamp and yadamp ( 2527).preparations of review articles or book chapters . the apd2 was very helpful to us in writing a review article on human antimicrobial peptides and proteins ( 47 ) . it also inspired us to write the first annual report for amps ( 48).interactions with the community . the apd provides a platform for us to regularly interact with users , reply to their inquiries and listen to their suggestions . users can search peptide sequence , source , activity , structure , chemical modification , peptide properties ( such as net charge , length , hydrophobic% , binding partners ) , the year of publication , author , mechanism of action and more . in addition to peptide length , net charge , amino acid composition and boman index previously programmed in the apd ( 16 ) , the apd3 enabled the calculations of molecular weight , molecular formula , molar extinction coefficient and gravy ( 35 ) . , the apd also enabled us to propose unified classification schemes for 3d structures as well as sequences of amps ( 9,31 ) . once a new peptide is sequenced , one would like to know which known sequences it most resembles . ( 36 ) found no homologous sequences for bactofencin a using the blast database , but identified similar sequences in the apd2 . the apd3 provides an average net charge of + 3.2 and length of 32.7 based on the 2619 amps . these statistical parameters are useful for describing the general properties of amps ( see also figure 1 and table 4 ) . cleavage sequence selection for recombinant amp expression . in the apd3 , there were 754 amps containing a methionine residue ( m ) and only 76 peptides containing a dp pair . such a dramatic difference formed the basis for our previous creation of a dp sequence as a cleavage site to release the recombinant form of human cathelicidin ll-37 from the expressed fusion protein by formic acid ( 37 ) . because less amps contain the dp site than m , this cleavage site can have a broader application in expression and purification of amps with a native sequence ( 38 ) . template selection for structure - activity relationship ( sar ) studies . to understand why a bacterial membrane anchor is not toxic , we used the apd to identify aurein 1.2 that shares the n - terminal glfd sequence with the membrane anchor ( 39 ) . peptide property improvements . based on the arginine / lysine ratio in amps with different activities , the antiviral peptides were found to have the highest arginine content compared to other activity groups . this finding enabled us to improve anti - hiv activity of known amps by introducing additional arginines ( 40 ) . based on the 525 entries in the apd ( 16 ) , loose developed the grammar approach ( 41 ) . using the apd2 , we developed a database filtering technology for peptide design ( 42 ) . by combining the most probable parameters derived from the database , we were able to obtain a potent peptide against methicillin - resistant s. aureus ( mrsa ) . since the abundant amino acids in the apd2 are glycines , lysines and leucines ( 17 ) , gellman ( 43 ) introduced a glycine - like unit into synthetic polymers , leading to improved cell selectivity ( i.e. more toxic against bacteria and less toxic to human cells ) . lata et al . ( 44 ) first used the apd sequences as a positive training set to program machine - learning algorithms for amp prediction . ( 45 ) tested a two - level multi - label classifier iamp-2l based on the multiple functions of amps annotated in the apd2 . found that the apd2 was able to predict more possible amps than existing machine - learning programs online ( 46 ) . as a new addition to the apd3 , users can access select peptide prediction programs directly from the apd links . construction of new databases . since the apd is an open resource , it allowed others to copy this database to build other databases such as camp , lamp and yadamp ( 2527 ) . the apd2 was very helpful to us in writing a review article on human antimicrobial peptides and proteins ( 47 ) . it also inspired us to write the first annual report for amps ( 48 ) . the apd provides a platform for us to regularly interact with users , reply to their inquiries and listen to their suggestions . in summary , the potential applications of the apd3 are beyond our descriptions above . with continued expansion and improvements of the database , since the publication of the apd in 2004 , multiple databases have been constructed with narrower or wider scopes ( for a recent review , see 49 ) . examples are bactibase for bacteriocins , phytamp for plant amps , dadp for amphibian peptides and penbase for shrimp amps ( 1822 ) . there are also databases for special types of amps such as defensins knowledgebase for defensins and cybase for circular polypeptides ( 23,24 ) . some recent databases have collected other sequences . while campr3 ( 27 ) collected 5390 predicted sequences without activity data , dbaasp2 collected 6000 synthetic peptides ( accessed in october 2015 ) ( 50 ) . for example , yang et al . ( 51 ) recently synthesized multiple predicted peptides and found little or no antimicrobial activity , while most of the isolated peptides are true amps . it is evident that the amp research has its niche in the  omics age . up or down regulation of amps is related to various human diseases ( 35 ) . together , amps from the host , commensal bacteria and invading pathogens shape our microbiota that can be linked to various human diseases ( 52 ) . as we illustrated above , the construction of well - annotated amp databases is helpful to the researchers in the field . during the past 13 years the 2619 amp entries in the current apd3 are almost five times those in the original apd . the apd3 registers peptides by following a set of criteria ( i.e. natural amps with a known sequence , activity and size less than 200 amino acids ) . we hope that such a well - registered data set can facilitate our effort in deciphering nature 's design principles of amps . for this goal , it is necessary not to mix natural amps with synthetic peptides so that the underlying features would not be masked , diluted or even distorted . we also decided to postpone collecting predicted sequences at this stage because such sequences may not be true amps . because there are different numbers of peptides in other databases ( 15,1827 ) , it is useful to address the following question before closing . how many amps with known activity have we discovered from natural sources as of oct 2015 ? indeed , a comparative analysis of over 10 amp databases in 2014 revealed 2497 natural sequences with validated antimicrobial activity ( 53 ) , which corresponded closely to the total number of the amps in our database then . we predict that the final number of natural amps will be at least in the million range if 1.3 million named species can each produce at least one such peptide . in conclusion , the apd3 is a comprehensive database for peptide discovery chronicle , nomenclature , classification , information search , calculations , prediction and design of amps .
the antimicrobial peptide database ( apd , http://aps.unmc.edu/ap/ ) is an original database initially online in 2003 . 
 the apd2 ( 2009 version ) has been regularly updated and further expanded into the apd3 . 
 this database currently focuses on natural antimicrobial peptides ( amps ) with defined sequence and activity . 
 it includes a total of 2619 amps with 261 bacteriocins from bacteria , 4 amps from archaea , 7 from protists , 13 from fungi , 321 from plants and 1972 animal host defense peptides . 
 the apd3 contains 2169 antibacterial , 172 antiviral , 105 anti - hiv , 959 antifungal , 80 antiparasitic and 185 anticancer peptides . 
 newly annotated are amps with antibiofilm , antimalarial , anti - protist , insecticidal , spermicidal , chemotactic , wound healing , antioxidant and protease inhibiting properties . 
 we also describe other searchable annotations , including target pathogens , molecule - binding partners , post - translational modifications and animal models . 
 amino acid profiles or signatures of natural amps are important for peptide classification , prediction and design . 
 finally , we summarize various database applications in research and education .