( ( ( Protons and ) neutrons ) ( ( are ( found ( at ( ( the ( core ( , ( or ( nucleus , ) ) ) ) ) ( of ( the atom ) ) ) ) ) ) . ) )
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (VP (VBN found) (PP (IN at) (NP (NP (DT the) (NN core) (, ,) (CC or) (NN nucleus) (, ,)) (PP (IN of) (NP (DT the) (NN atom))))))) (. .)))
Protons and neutrons  are found at the core, or nucleus, of the atom.
(ROOT (S (NP (NP (DT The) (NN atom)) (PP (IN in) (NP (DT a) (NN neutron)))) (VP (VBZ is) (VP (VBN found) (PP (IN in) (NP (DT the) (DT the) (NN nucleus))))) (. .)))