A polypeptide comprising a complement factor B protein analog, wherein: the complement factor B analog comprises a substitution of a free cysteine amino acid; the free cysteine corresponds to amino acid 292 of SEQ ID NO:1, as determined by alignment of the amino acid sequence of the complement factor B analog with the amino acid sequence of SEQ ID NO: 1; the human complement factor B protein analog is at least 90% identical to amino acids 26-764 of SEQ ID NOs: 1, 2 or 3; to amino acids 26-990 of SEQ ID NOs: 22 or 23; to amino acids 26-480 of SEQ ID NO: 2; or to amino acids 26-1003 of SEQ ID NO:26; and said complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein encoded by a mammalian genome, and said complement factor B protein analog (i) has diminished protease activity as compared to the corresponding native complement factor B protein; (ii) has diminished ability to be cleaved by factor D protein as compared to the corresponding native complement factor B protein; or (iii) has diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or (iv) can compete with a native factor B for binding to factor D. the complement factor B analog comprises a substitution of a free cysteine amino acid; the free cysteine corresponds to amino acid 292 of SEQ ID NO:1, as determined by alignment of the amino acid sequence of the complement factor B analog with the amino acid sequence of SEQ ID NO: 1; the human complement factor B protein analog is at least 90% identical to amino acids 26-764 of SEQ ID NOs: 1, 2 or 3; to amino acids 26-990 of SEQ ID NOs: 22 or 23; to amino acids 26-480 of SEQ ID NO: 2; or to amino acids 26-1003 of SEQ ID NO:26; and said complement factor B protein analog has increased C3b binding affinity as compared to a corresponding native complement factor B protein encoded by a mammalian genome, and said complement factor B protein analog (i) has diminished protease activity as compared to the corresponding native complement factor B protein; (ii) has diminished ability to be cleaved by factor D protein as compared to the corresponding native complement factor B protein; or (iii) has diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or (iv) can compete with a native factor B for binding to factor D. (i) has diminished protease activity as compared to the corresponding native complement factor B protein; (ii) has diminished ability to be cleaved by factor D protein as compared to the corresponding native complement factor B protein; or (iii) has diminished protease activity as compared to the corresponding native complement factor B protein and diminished ability to be cleaved by a factor D protein as compared to the corresponding native complement factor B protein; or (iv) can compete with a native factor B for binding to factor D.