The prefix at-, when used with verbs of movement, means a direction from one place towards another specific place (usually the subject is in the latter place).

ateiti - to come
atbėgti - to come (by running)
atvažiuoti - to come (by a transport)
atskristi - to come (by flying)
atjoti - to come (by riding)
atplaukti - to come (by swimming)

You may find these directions confusing. The best examples explaining them are English words to go and to come. Prefixless eiti means to go, and ateiti means to come.

Aš einu į mokyklą. I am going to school.
Aš ateinu į mokyklą. I come to school.
Dėstytojas ateina į universitetą. The lecturer comes to the university.
Studentai atbėga į paskaitą. Students come (by running) to the lecture.
Laivas plaukia į Klaipėdą. The ship is "swimming" to Klaipėda.
Laivas atplaukia į Klaipėdą. The ship comes (by "swimming") to Klaipėda.