@article{
 title = {How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal},
 type = {article},
 year = {2019},
 pages = {1-23},
 id = {ee4b8473-2505-313c-9dd4-2ef614aeeede},
 created = {2019-10-30T11:01:35.375Z},
 file_attached = {false},
 profile_id = {5c1040db-25e3-36ea-a919-0994a44709e7},
 group_id = {c4af41cc-7e3c-3fd3-9982-bdb923596eee},
 last_modified = {2020-09-08T15:25:48.994Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Smith2019},
 private_publication = {false},
 abstract = {Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.},
 bibtype = {article},
 author = {Smith, Pete and Soussana, Jean‐Francois and Angers, Denis and Schipper, Louis and Chenu, Claire and Rasse, Daniel P. and Batjes, Niels H. and Egmond, Fenny and McNeill, Stephen and Kuhnert, Matthias and Arias‐Navarro, Cristina and Olesen, Jorgen E. and Chirinda, Ngonidzashe and Fornara, Dario and Wollenberg, Eva and Álvaro‐Fuentes, Jorge and Sanz‐Cobena, Alberto and Klumpp, Katja},
 doi = {10.1111/gcb.14815},
 journal = {Global Change Biology},
 number = {August}
}

{"_id":"vXARLQDHn2ZRZMkKf","bibbaseid":"smith-soussana-angers-schipper-chenu-rasse-batjes-egmond-etal-howtomeasurereportandverifysoilcarbonchangetorealizethepotentialofsoilcarbonsequestrationforatmosphericgreenhousegasremoval-2019","authorIDs":[],"author_short":["Smith, P.","Soussana, J.","Angers, D.","Schipper, L.","Chenu, C.","Rasse, D., P.","Batjes, N., H.","Egmond, F.","McNeill, S.","Kuhnert, M.","Arias‐Navarro, C.","Olesen, J., E.","Chirinda, N.","Fornara, D.","Wollenberg, E.","Álvaro‐Fuentes, J.","Sanz‐Cobena, A.","Klumpp, K."],"bibdata":{"title":"How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal","type":"article","year":"2019","pages":"1-23","id":"ee4b8473-2505-313c-9dd4-2ef614aeeede","created":"2019-10-30T11:01:35.375Z","file_attached":false,"profile_id":"5c1040db-25e3-36ea-a919-0994a44709e7","group_id":"c4af41cc-7e3c-3fd3-9982-bdb923596eee","last_modified":"2020-09-08T15:25:48.994Z","read":false,"starred":false,"authored":false,"confirmed":"true","hidden":false,"citation_key":"Smith2019","private_publication":false,"abstract":"Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.","bibtype":"article","author":"Smith, Pete and Soussana, Jean‐Francois and Angers, Denis and Schipper, Louis and Chenu, Claire and Rasse, Daniel P. and Batjes, Niels H. and Egmond, Fenny and McNeill, Stephen and Kuhnert, Matthias and Arias‐Navarro, Cristina and Olesen, Jorgen E. and Chirinda, Ngonidzashe and Fornara, Dario and Wollenberg, Eva and Álvaro‐Fuentes, Jorge and Sanz‐Cobena, Alberto and Klumpp, Katja","doi":"10.1111/gcb.14815","journal":"Global Change Biology","number":"August","bibtex":"@article{\n title = {How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal},\n type = {article},\n year = {2019},\n pages = {1-23},\n id = {ee4b8473-2505-313c-9dd4-2ef614aeeede},\n created = {2019-10-30T11:01:35.375Z},\n file_attached = {false},\n profile_id = {5c1040db-25e3-36ea-a919-0994a44709e7},\n group_id = {c4af41cc-7e3c-3fd3-9982-bdb923596eee},\n last_modified = {2020-09-08T15:25:48.994Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Smith2019},\n private_publication = {false},\n abstract = {Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-α-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 Å for the interface backbone atoms) increased from 21% with default Glide SP settings to 58% with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63% success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40% of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.},\n bibtype = {article},\n author = {Smith, Pete and Soussana, Jean‐Francois and Angers, Denis and Schipper, Louis and Chenu, Claire and Rasse, Daniel P. and Batjes, Niels H. and Egmond, Fenny and McNeill, Stephen and Kuhnert, Matthias and Arias‐Navarro, Cristina and Olesen, Jorgen E. and Chirinda, Ngonidzashe and Fornara, Dario and Wollenberg, Eva and Álvaro‐Fuentes, Jorge and Sanz‐Cobena, Alberto and Klumpp, Katja},\n doi = {10.1111/gcb.14815},\n journal = {Global Change Biology},\n number = {August}\n}","author_short":["Smith, P.","Soussana, J.","Angers, D.","Schipper, L.","Chenu, C.","Rasse, D., P.","Batjes, N., H.","Egmond, F.","McNeill, S.","Kuhnert, M.","Arias‐Navarro, C.","Olesen, J., E.","Chirinda, N.","Fornara, D.","Wollenberg, E.","Álvaro‐Fuentes, J.","Sanz‐Cobena, A.","Klumpp, K."],"biburl":"https://bibbase.org/service/mendeley/5c1040db-25e3-36ea-a919-0994a44709e7","bibbaseid":"smith-soussana-angers-schipper-chenu-rasse-batjes-egmond-etal-howtomeasurereportandverifysoilcarbonchangetorealizethepotentialofsoilcarbonsequestrationforatmosphericgreenhousegasremoval-2019","role":"author","urls":{},"metadata":{"authorlinks":{}},"downloads":0},"bibtype":"article","creationDate":"2019-10-30T12:06:14.756Z","downloads":0,"keywords":[],"search_terms":["measure","report","verify","soil","carbon","change","realize","potential","soil","carbon","sequestration","atmospheric","greenhouse","gas","removal","smith","soussana","angers","schipper","chenu","rasse","batjes","egmond","mcneill","kuhnert","arias‐navarro","olesen","chirinda","fornara","wollenberg","álvaro‐fuentes","sanz‐cobena","klumpp"],"title":"How to measure, report and verify soil carbon change to realize the potential of soil carbon sequestration for atmospheric greenhouse gas removal","year":2019,"biburl":"https://bibbase.org/service/mendeley/5c1040db-25e3-36ea-a919-0994a44709e7","dataSources":["LRSiZxnRXfxznxXRS","ya2CyA73rpZseyrZ8","2252seNhipfTmjEBQ"]}