{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T19:19:46Z","timestamp":1773343186245,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The typical workflow for NMR structure determination involves collecting thousands of conformational restraints, calculating a bundle of 20\u201340 conformers in agreement with them and refining the energetics of these conformers. The structure calculation step employs simulated annealing based on molecular dynamics (MD) simulations with very simplified force fields. The value of refining the calculated conformers using restrained MD (rMD) simulations with state-of-art force fields is documented. This refinement however presents various subtleties, from the proper formatting of conformational restraints to the definition of suitable protocols.<\/jats:p>\n               <jats:p>Results: We describe a web interface to set up and run calculations with the AMBER package, which we called AMPS-NMR (AMBER-based Portal Server for NMR structures). The interface allows the refinement of NMR structures through rMD. Some predefined protocols are provided for this purpose, which can be personalized; it is also possible to create an entirely new protocol. AMPS-NMR can handle various restraint types. Standard rMD refinement in explicit water of the structures of three different proteins are shown as examples. AMPS-NMR additionally includes a workspace for the user to store different calculations. As an ancillary service, a web interface to AnteChamber is available, enabling the calculation of force field parameters for organic molecules such as ligands in protein\u2013ligand adducts.<\/jats:p>\n               <jats:p>Availability and Implementation: AMPS-NMR is embedded within the NMR services of the WeNMR project and is available at http:\/\/py-enmr.cerm.unifi.it\/access\/index\/amps-nmr; its use requires registration with a digital certificate.<\/jats:p>\n               <jats:p>Contact: \u00a0ivanobertini@cerm.unifi.it<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr415","type":"journal-article","created":{"date-parts":[[2011,7,15]],"date-time":"2011-07-15T00:34:59Z","timestamp":1310690099000},"page":"2384-2390","source":"Crossref","is-referenced-by-count":56,"title":["A Grid-enabled web portal for NMR structure refinement with AMBER"],"prefix":"10.1093","volume":"27","author":[{"given":"Ivano","family":"Bertini","sequence":"first","affiliation":[{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"},{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A.","family":"Case","sequence":"additional","affiliation":[{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"},{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucio","family":"Ferella","sequence":"additional","affiliation":[{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Giachetti","sequence":"additional","affiliation":[{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 2Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy, 3BioMaPS Institute and 4Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Rd., Piscataway NJ 08854-8087, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Antonio","family":"Rosato","sequence":"additional","affiliation":[{"name":"1 Magnetic Resonance Center (CERM), University of Florence, Via L. 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