Protein Engineering Design & Selection is indexed in Biological Abstracts, BIOSIS Previews, Biotechnology and Bioengineering Abstracts, Biotechnology Citation Index, CAB Abstracts, Chemical Abstracts, Current Contents, EMBASE, Environmental Science and Pollution Management, Food Science and Technology Abstracts, Journal Citation Reports, ProQuest, and Science Citation Index. According to the latest Journal Citation Reports, the journal has a 2019 impact factor of 1.774, ranking it 247th out of 297 in the category "Biochemistry & Molecular Biology" and 120th out of 156 in the category "Biotechnology & Applied Microbiology".
