. 2018 Mar 13;114(5):1009–1017. doi: 10.1016/j.bpj.2018.01.020

Table 1.

Comparative Protein Dynamics Analyses Conducted with DROIDS

Category	Protein	PDB ID	Species	Sequence Similarity (%)	Grantham Distance (Average)	Dynamic Similarity (Average dFLUX)
Adaptive ortholog	p450 cytochrome	1f4t-1phd	Sulfolobus solfactaricus	15.95	79.93	0.28
Adaptive ortholog	p450 cytochrome	1f4t-1phd	Pseudomonas putida	15.95	79.93	0.28
Adaptive ortholog	p450 cytochrome	1n97-1phd	Thermus thermophilus	10.88	82.10	0.25
Adaptive ortholog	p450 cytochrome	1n97-1phd	P. putida	10.88	82.10	0.25
Adaptive ortholog	p450 cytochrome	1t2b-1phd	Citrobacter braakii	23.68	76.63	0.27
Adaptive ortholog	p450 cytochrome	1t2b-1phd	P. putida	23.68	76.63	0.27
Adaptive ortholog	DNA polymerase	4n56-1kfd	Thermus aquaticus	29.1	77.86	0.89
Adaptive ortholog	DNA polymerase	4n56-1kfd	E. coli	29.1	77.86	0.89
Functional ortholog	alcohol dehydrogenase	1htb-6adh	Homo sapiens	86.91	66.47	0.02
Functional ortholog	alcohol dehydrogenase	1htb-6adh	Equus caballus	86.91	66.47	0.02
Functional ortholog	NBD1 domain of CFTR	1xf9-2pze	Mus musculus	83.12	52.58	0.29
Functional ortholog	NBD1 domain of CFTR	1xf9-2pze	H. sapiens	83.12	52.58	0.29
Functional ortholog	L-Dap aminotransferase	3ei7-3qgu	Arabidopsis thaliana
Functional ortholog	L-Dap aminotransferase	3ei7-3qgu	Chalmydomonas reinhardtii
Functional ortholog	ATP-free CFTR	5uar-5uak	Danio rerio	68.61	53.26	0.04
Functional ortholog	ATP-free CFTR	5uar-5uak	H. sapiens	68.61	53.26	0.04
Functional paralog	lyase (DCoH2 and DCoH)	1ru0-1dch	M. musculus	66.68	52.10	0.02
Functional paralog	lyase (DCoH2 and DCoH)	1ru0-1dch	Rattus norvegicus	66.68	52.10	0.02
Functional paralog	serine proteases (Trypsin and pancreatic elastase)	2ptn-3est	Bos taurus	35.43	75.96	0.06
Functional paralog	serine proteases (Trypsin and pancreatic elastase)	2ptn-3est	Sus scrofa	35.43	75.96	0.06
Functional paralog	interferon regulatory factors (IRF-5 and IRF-3)	3dsh-1j2f	H. sapiens	23.90	84.27	0.29
nsSNV disease	V599E mutant of B-RAF kinase (melanoma)	1uwj-1uwh	H. sapiens	99.29	113.50	0.73
nsSNV disease	F508R disease and F508S nondisease mutant of NBD1 domain of CFTR (cystic fibrosis)	1xfa-1xf9	H. sapiens	99.65	110.00	1.28
nsSNV disease	F508R disease and wild-type NBD1 domain of CFTR (cystic fibrosis)	1xfa-2pze	H. sapiens	93.12	51.05	1.54
nsSNV disease	ΔF508 disease and wild-type NBD1 domain of CFTR (cystic fibrosis)	2pzf-2pze	H. sapiens	99.57	NA	0.51
nsSNV disease	Htt36Q3H and Htt17Q (Huntington’s disease)	4fec-3iou	H. sapiens	97.37	76.27	0.05
nsSNV disease	PrP226 and human prion protein (prion-based amyloid disease)	5l6r-1qlx	H. sapiens	96.24	99.75	0.09
Null comparison	collagen	1bkv	H. sapiens	100	0%	0.12
Null comparison	collagen-like peptide	1cag	H. sapiens	100	0%	0.17
Null comparison	DNA polymerase (Klenow fragment)	1kfd	E. coli	100	0%	0.13
Null comparison	T4 lysozyme	1lyd	E. virus T4	100	0%	0.15
Null comparison	ubiquitin	1ubq	H. sapiens	100	0%	0.04
Null comparison	pancreatic elastase	3est	S. scrofa	100	0%	0.06
Phosphorylation	phosphorylated IRF-3 and dephosphorylated IRF-3	3a77-1j2f	H. sapiens	98.68	0%	0.02
Phosphorylation	phosphorylated DesR (inactive) and dephosphorylated DesR (active)	4le1-4le2	Bacillus subtilis	100	0%	0.06
Disulfide (S-S)	proinsulin (with and without three disulfide bonds)	2kqp	H. sapiens	100	0%	0.63
Disulfide (S-S)	T4 lysozyme with and without a bioengineered disulfide bond)	1l35-1lyd	E. virus T4	100	0%	0.08 (0.47) at site of S-S

The impacts of genetic mutation on each protein are compared at the levels of amino acid sequence and chemical distance, as well as MD. This data is summarized in Figure 2. ID, identifier; NA, not applicable.