title: NMRFAM-SDF: a protein structure determination framework.
abstract: The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Hesam
authors.initials: H
authors.lastname: Dashti
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Woonghee
authors.initials: W
authors.lastname: Lee
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Marco
authors.initials: M
authors.lastname: Tonelli
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Claudia C
authors.initials: CC
authors.lastname: Cornilescu
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Cornilescu
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Fariba M
authors.initials: FM
authors.lastname: Assadi-Porter
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: William M
authors.initials: WM
authors.lastname: Westler
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA.
authors.forename: Hamid R
authors.initials: HR
authors.lastname: Eghbalnia
authors.affiliation: National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, USA. markley@nmrfam.wisc.edu.
authors.forename: John L
authors.initials: JL
authors.lastname: Markley
mesh_terms: D066241:Carbon-13 Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D064878:Web Browser; D057188:Workflow
chemical_list: D011506:Proteins
keywords: ADAPT-NMR; ARECA; Automated protein structure determination framework; CASD-NMR; Non-uniform sampling; PINE; PONDEROSA-C/S; Validation