| Server/ URL . | Functionalitya . | Inputs . | Outputs . | Vab . | Advantages . | Limitations . | Year . |
|---|---|---|---|---|---|---|---|
| Detects multiple protein systems | |||||||
| mCSM-lig http://structure.bioc.cam.ac.uk/mcsm_lig | Quantify the effects of mutations on PLIs | PDB file or code, mutation chain, mutation, ligand, and WT affinity | ∆∆G, stability outcome, visible complex structure | Y | Provides insights into understanding mendelian disease mutations | The accuracy of forecasts needs to be improved | 2016 |
| AIMMS http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/ | Scan mutations for protein targets | Task name, complex PDB file, ligand name, parameter file mutation details and e-mail | ∆∆G, heatmap | N | The first online platform for de novo drug resistance prediction of any protein–ligand system | More complex operations than other tools in the same category | 2020 |
| PremPLI https://lilab.jysw.suda.edu.cn/research/PremPLI/ | Estimate the effects of mutations on PLIs | PDB file or code, protein, chain, ligand, position, and mutation | ∆∆G and interface | Y | Requires lesser computational resources, allows large-scale mutation scan | Mutation lists are not allowed | 2021 |
| Detects specific protein systems | |||||||
| KRDS http://bcbl.kaist.ac.kr/KRDS/ | Evaluate DRMs in kinase | Job name, e-mail, PDB file, ligand file, drug binding site and mutation | Docking scores and figure, drug-bound structure | Y | Easy to use | Spend more time | 2018 |
| SUSPECT-PZA http://biosig.unimelb.edu.au/suspect_pza/ | Predict PZA resistance mutations in pncA | Mutation details | Predicted outcome, WT environment, parameters by other softwares, experimental evidence and interactive view | Y | Included structural information of the WT residue | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-BDQ http://biosig.unimelb.edu.au/suspect_bdq/ | Identify bedaquiline resistance mutations in AtpE | Mutation details | Predicted outcome, WT environment, parameters by other softwares and interactive view | Y | Identify novel Bedaquiline resistance mutations | The accuracy of forecasts needs to be improved | 2019 |
| SUSPECT-RIF https://biosig.unimelb.edu.au/suspect_rif/ | Identify rifampicin resistance mutation | Organism and mutation details | Predicted outcome, WT environment, distance information and interactive view | Y | Outperforming the current gold-standard GeneXpert-MTB/RIF | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-ABL http://biosig.unimelb.edu.au/suspect_abl/ | Predict DRMs in Abelson 1 kinase | Inhibitors and mutation details | Predicted outcome, ∆∆G, WT environment, conservation scores, pharmacophore changes and interactive view | Y | Visualization of molecular interactions within the WT and MT residue environment | The accuracy of forecasts needs to be improved | 2021 |
| Server/ URL . | Functionalitya . | Inputs . | Outputs . | Vab . | Advantages . | Limitations . | Year . |
|---|---|---|---|---|---|---|---|
| Detects multiple protein systems | |||||||
| mCSM-lig http://structure.bioc.cam.ac.uk/mcsm_lig | Quantify the effects of mutations on PLIs | PDB file or code, mutation chain, mutation, ligand, and WT affinity | ∆∆G, stability outcome, visible complex structure | Y | Provides insights into understanding mendelian disease mutations | The accuracy of forecasts needs to be improved | 2016 |
| AIMMS http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/ | Scan mutations for protein targets | Task name, complex PDB file, ligand name, parameter file mutation details and e-mail | ∆∆G, heatmap | N | The first online platform for de novo drug resistance prediction of any protein–ligand system | More complex operations than other tools in the same category | 2020 |
| PremPLI https://lilab.jysw.suda.edu.cn/research/PremPLI/ | Estimate the effects of mutations on PLIs | PDB file or code, protein, chain, ligand, position, and mutation | ∆∆G and interface | Y | Requires lesser computational resources, allows large-scale mutation scan | Mutation lists are not allowed | 2021 |
| Detects specific protein systems | |||||||
| KRDS http://bcbl.kaist.ac.kr/KRDS/ | Evaluate DRMs in kinase | Job name, e-mail, PDB file, ligand file, drug binding site and mutation | Docking scores and figure, drug-bound structure | Y | Easy to use | Spend more time | 2018 |
| SUSPECT-PZA http://biosig.unimelb.edu.au/suspect_pza/ | Predict PZA resistance mutations in pncA | Mutation details | Predicted outcome, WT environment, parameters by other softwares, experimental evidence and interactive view | Y | Included structural information of the WT residue | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-BDQ http://biosig.unimelb.edu.au/suspect_bdq/ | Identify bedaquiline resistance mutations in AtpE | Mutation details | Predicted outcome, WT environment, parameters by other softwares and interactive view | Y | Identify novel Bedaquiline resistance mutations | The accuracy of forecasts needs to be improved | 2019 |
| SUSPECT-RIF https://biosig.unimelb.edu.au/suspect_rif/ | Identify rifampicin resistance mutation | Organism and mutation details | Predicted outcome, WT environment, distance information and interactive view | Y | Outperforming the current gold-standard GeneXpert-MTB/RIF | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-ABL http://biosig.unimelb.edu.au/suspect_abl/ | Predict DRMs in Abelson 1 kinase | Inhibitors and mutation details | Predicted outcome, ∆∆G, WT environment, conservation scores, pharmacophore changes and interactive view | Y | Visualization of molecular interactions within the WT and MT residue environment | The accuracy of forecasts needs to be improved | 2021 |
aAbbreviation: PLIs: Protein–Ligand Interactions, DRMs: Drug resistance mutations.
bWhether the visualization of network is supported in each tool.
| Server/ URL . | Functionalitya . | Inputs . | Outputs . | Vab . | Advantages . | Limitations . | Year . |
|---|---|---|---|---|---|---|---|
| Detects multiple protein systems | |||||||
| mCSM-lig http://structure.bioc.cam.ac.uk/mcsm_lig | Quantify the effects of mutations on PLIs | PDB file or code, mutation chain, mutation, ligand, and WT affinity | ∆∆G, stability outcome, visible complex structure | Y | Provides insights into understanding mendelian disease mutations | The accuracy of forecasts needs to be improved | 2016 |
| AIMMS http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/ | Scan mutations for protein targets | Task name, complex PDB file, ligand name, parameter file mutation details and e-mail | ∆∆G, heatmap | N | The first online platform for de novo drug resistance prediction of any protein–ligand system | More complex operations than other tools in the same category | 2020 |
| PremPLI https://lilab.jysw.suda.edu.cn/research/PremPLI/ | Estimate the effects of mutations on PLIs | PDB file or code, protein, chain, ligand, position, and mutation | ∆∆G and interface | Y | Requires lesser computational resources, allows large-scale mutation scan | Mutation lists are not allowed | 2021 |
| Detects specific protein systems | |||||||
| KRDS http://bcbl.kaist.ac.kr/KRDS/ | Evaluate DRMs in kinase | Job name, e-mail, PDB file, ligand file, drug binding site and mutation | Docking scores and figure, drug-bound structure | Y | Easy to use | Spend more time | 2018 |
| SUSPECT-PZA http://biosig.unimelb.edu.au/suspect_pza/ | Predict PZA resistance mutations in pncA | Mutation details | Predicted outcome, WT environment, parameters by other softwares, experimental evidence and interactive view | Y | Included structural information of the WT residue | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-BDQ http://biosig.unimelb.edu.au/suspect_bdq/ | Identify bedaquiline resistance mutations in AtpE | Mutation details | Predicted outcome, WT environment, parameters by other softwares and interactive view | Y | Identify novel Bedaquiline resistance mutations | The accuracy of forecasts needs to be improved | 2019 |
| SUSPECT-RIF https://biosig.unimelb.edu.au/suspect_rif/ | Identify rifampicin resistance mutation | Organism and mutation details | Predicted outcome, WT environment, distance information and interactive view | Y | Outperforming the current gold-standard GeneXpert-MTB/RIF | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-ABL http://biosig.unimelb.edu.au/suspect_abl/ | Predict DRMs in Abelson 1 kinase | Inhibitors and mutation details | Predicted outcome, ∆∆G, WT environment, conservation scores, pharmacophore changes and interactive view | Y | Visualization of molecular interactions within the WT and MT residue environment | The accuracy of forecasts needs to be improved | 2021 |
| Server/ URL . | Functionalitya . | Inputs . | Outputs . | Vab . | Advantages . | Limitations . | Year . |
|---|---|---|---|---|---|---|---|
| Detects multiple protein systems | |||||||
| mCSM-lig http://structure.bioc.cam.ac.uk/mcsm_lig | Quantify the effects of mutations on PLIs | PDB file or code, mutation chain, mutation, ligand, and WT affinity | ∆∆G, stability outcome, visible complex structure | Y | Provides insights into understanding mendelian disease mutations | The accuracy of forecasts needs to be improved | 2016 |
| AIMMS http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/ | Scan mutations for protein targets | Task name, complex PDB file, ligand name, parameter file mutation details and e-mail | ∆∆G, heatmap | N | The first online platform for de novo drug resistance prediction of any protein–ligand system | More complex operations than other tools in the same category | 2020 |
| PremPLI https://lilab.jysw.suda.edu.cn/research/PremPLI/ | Estimate the effects of mutations on PLIs | PDB file or code, protein, chain, ligand, position, and mutation | ∆∆G and interface | Y | Requires lesser computational resources, allows large-scale mutation scan | Mutation lists are not allowed | 2021 |
| Detects specific protein systems | |||||||
| KRDS http://bcbl.kaist.ac.kr/KRDS/ | Evaluate DRMs in kinase | Job name, e-mail, PDB file, ligand file, drug binding site and mutation | Docking scores and figure, drug-bound structure | Y | Easy to use | Spend more time | 2018 |
| SUSPECT-PZA http://biosig.unimelb.edu.au/suspect_pza/ | Predict PZA resistance mutations in pncA | Mutation details | Predicted outcome, WT environment, parameters by other softwares, experimental evidence and interactive view | Y | Included structural information of the WT residue | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-BDQ http://biosig.unimelb.edu.au/suspect_bdq/ | Identify bedaquiline resistance mutations in AtpE | Mutation details | Predicted outcome, WT environment, parameters by other softwares and interactive view | Y | Identify novel Bedaquiline resistance mutations | The accuracy of forecasts needs to be improved | 2019 |
| SUSPECT-RIF https://biosig.unimelb.edu.au/suspect_rif/ | Identify rifampicin resistance mutation | Organism and mutation details | Predicted outcome, WT environment, distance information and interactive view | Y | Outperforming the current gold-standard GeneXpert-MTB/RIF | The accuracy of forecasts needs to be improved | 2020 |
| SUSPECT-ABL http://biosig.unimelb.edu.au/suspect_abl/ | Predict DRMs in Abelson 1 kinase | Inhibitors and mutation details | Predicted outcome, ∆∆G, WT environment, conservation scores, pharmacophore changes and interactive view | Y | Visualization of molecular interactions within the WT and MT residue environment | The accuracy of forecasts needs to be improved | 2021 |
aAbbreviation: PLIs: Protein–Ligand Interactions, DRMs: Drug resistance mutations.
bWhether the visualization of network is supported in each tool.
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