Namdinator - Automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

TY - JOUR

T1 - Namdinator - Automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

AU - Kidmose, Rune Thomas

AU - Juhl, Jonathan

AU - Nissen, Poul

AU - Boesen, Thomas

AU - Karlsen, Jesper Lykkegaard

AU - Pedersen, Bjørn Panyella

PY - 2019

Y1 - 2019

N2 - Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool..

AB - Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool..

KW - automation

KW - cryo-EM

KW - crystallography

KW - flexible fitting

KW - MDFF

KW - model-fitting

KW - molecular dynamics

KW - molecular dynamics flexible fitting

KW - web services

UR - http://www.scopus.com/inward/record.url?scp=85068206269&partnerID=8YFLogxK

U2 - 10.1107/S2052252519007619

DO - 10.1107/S2052252519007619

M3 - Journal article

C2 - 31316797

AN - SCOPUS:85068206269

SN - 2052-2525

VL - 6

SP - 526

EP - 531

JO - IUCrJ

JF - IUCrJ

IS - 4

ER -