PCA-MutPred

Features used in the prediciton of binding free energy change (ΔΔG) of protein-carbohydrate complexes

Sequence-based features
Feature number	Property ID	Property Description
Physicochemical properties of amino acid residues (69) (Chaudhary et al. 2015)
1	K0	Compressibility
2	Ht	Thermodynamic transfer hydrophobicity
3	Hp	Surrounding hydrophobicity
4	P	Polarity
5	pHi	Isoelectric point
6	pK'	Equilibrium constant with reference to the ionization property of COOH group
7	Mw	Molecular weight
8	Bl	Bulkiness
9	Rf	Chromatographic index
10	Mu	Refractive index
11	Hnc	Normalized consensus hydrophobicity
12	Pb	Beta-helical tendency
13	Pc	Coil tendency
14	Ra	Solvent accessible reduction ratio
15	V0	Partial-specific volume
16	Nl	Average long-range contacts
17	dGh	Gibbs free energy change of hydration for unfolding
18	-TdSh	Unfolding entropy change of hydration
19	dCph	Unfolding hydration heat capacity change
20	-TdSc	Unfolding entropy change of chain
21	-TdS	Unfolding entropy change
22	s	Shape (position of branch point in a side-chain)
23	GEIM800105	Beta-strand indices (Geisow-Roberts, 1980)
24	GRAR740102	Polarity (Grantham, 1974)
25	GRAR740103	Volume (Grantham, 1974)
26	HOPA770101	Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982)
27	ISOY800102	Normalized relative frequency of extended structure (Isogai et al., 1980)
28	ISOY800103	Normalized relative frequency of bend (Isogai et al., 1980)
29	KANM800102	Average probability of beta-sheet (Kanehisa-Tsong, 1980)
30	KANM800103	Average probability of inner helix (Kanehisa-Tsong, 1980)
31	KARP850101	Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985)
32	KRIW790101	van der Waals interactions between side chains (Krigbaum-Komoriya, 1979)
33	LEVM760101	Hydrophobic parameter (Levitt, 1976)
34	LIFS790101	Conformational preference for all beta-strands (Lifson-Sander, 1979)
35	LIFS790103	Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979)
36	MANP780101	Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978)
37	MAXF760102	Normalized frequency of extended structure (Maxfield-Scheraga, 1976)
38	MAXF760106	Normalized frequency of alpha region (Maxfield-Scheraga, 1976)
39	MIYS850101	Effective partition energy (Miyazawa-Jernigan, 1985)
40	NAGK730102	Normalized frequency of beta-structure (Nagano, 1973)
41	NAGK730103	Normalized frequency of coil (Nagano, 1973)
42	BURA740102	Normalized frequency of extended structure (Burgess et al., 1974)
43	ARGP820101	Hydrophobicity index (Argos et al., 1982)
44	OOBM770103	Long range non-bonded energy per atom (Oobatake-Ooi, 1977)
45	OOBM850103	Optimized free energy transfer (Oobatake et al., 1985)
46	CHAM820101	Polarizability parameter (Charton-Charton, 1982)
47	OOBM850105	Optimized side chain interaction parameter (Oobatake et al., 1985)
48	PONP800102	Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980)
49	PONP800107	Accessibility reduction ratio (Ponnuswamy et al., 1980)
50	PRAM900104	Relative frequency in reverse-turn (Prabhakaran, 1990)
51	ROSM880102	Side chain hydropathy, corrected for solvation (Roseman, 1988)
52	SIMZ760101	Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982)
53	CHOP780202	Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
54	ZIMJ680101	Hydrophobicity (Zimmerman et al., 1968)
55	ZIMJ680102	Bulkiness (Zimmerman et al., 1968)
56	ZIMJ680105	RF rank (Zimmerman et al., 1968)
57	ONEK900102	Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990)
58	VINM940101	Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
59	KUHL950101	Hydrophilicity scale (Kuhn et al., 1995)
60	ZHOH040101	The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou, 2004)
61	ZHOH040102	The relative stability scale extracted from mutation experiments (Zhou-Zhou, 2004)
62	ZHOH040103	Hydrophobicity of residues (Zhou-Zhou, 2004)
63	PONJ960101	Average volumes of residues (Pontius et al., 1996)
64	WOLR790101	Hydrophobicity index (Wolfenden et al., 1979)
65	MIYS990101	Relative partition energies derived by the Bethe approximation (Miyazawa-Jernigan, 1999)
66	EISD860101	Solvation free energy (Eisenberg-McLachlan, 1986)
67	FASG760101	Molecular weight (Fasman, 1976)
68	FASG760102	Melting point (Fasman, 1976)
69	FAUJ830101	Hydrophobic parameter pi (Fauchere-Pliska, 1983)
	AAIndex2 (30)	Amino acid mutation matrices
70	ALTS910101	The PAM-120 matrix (Altschul, 1991)
71	BENS940104	Genetic code matrix (Benner et al., 1994)
72	CSEM940101	Residue replace ability matrix (Cserzo et al., 1994)
73	DAYM780301	Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
74	FITW660101	Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
75	GEOD900101	Hydrophobicity scoring matrix (George et al., 1990)
76	GONG920101	The mutation matrix for initially aligning (Gonnet et al., 1992)
77	GRAR740104	Chemical distance (Grantham, 1974)
78	HENS920102	BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
79	JOHM930101	Structure-based amino acid scoring table (Johnson-Overington, 1993)
80	KOLA920101	Conformational similarity index (Kolaskar-Kulkarni-Kale, 1992)
81	LEVJ860101	The secondary structure similarity matrix (Levin et al., 1986)
82	MCLA710101	The similarity of pairs of amino acids (McLachlan, 1971)
83	MCLA720101	Optimized free energy of transfer (McLachlan, 1972)
84	MIYS930101	Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
85	MIYT790101	Amino acid pair distance (Miyata et al., 1979)
86	RISJ880101	Scoring matrix (Risler et al., 1988)
87	TUDE900101	isomorphicity of replacements (Tudos et al., 1990)
88	AZAE970101	The single residue substitution matrix from interchanges of spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
89	AZAE970102	The substitution matrix derived from spatially conserved motifs (Azarya-Sprinzak et al., 1997)
90	RIER950101	Hydrophobicity scoring matrix (Riek et al., 1995)
91	KOSJ950109	Substitution matrices for alpha helix (Koshi-Goldstein, 1995)
92	KOSJ950110	Substitution matrices for beta sheet (Koshi-Goldstein, 1995)
93	KOSJ950111	Substitution matrices for turn (Koshi-Goldstein, 1995)
94	KOSJ950112	Substitution matrices for coil (Koshi-Goldstein, 1995)
95	KOSJ950113	Substitution matrices for exposed residues (Koshi-Goldstein, 1995)
96	KOSJ950114	Substitution matrices for buried residues (Koshi-Goldstein, 1995)
97	KOSJ950115	Substitution matrices for all residues (Koshi-Goldstein, 1995)
98	DOSZ010103	An amino acid similarity matrix based on the THREADER force field (Dosztanyi-Torda, 2001)
99	NAOD960101	Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
	AAIndex3 (14)	Amino acid pair-wise contact potentials
100	TANS760101	Statistical contact potential derived from 25 x-ray protein structures
101	ROBB790102	Interaction energies derived from side chain contacts in the interiors of known protein structures
102	BRYS930101	Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
103	MIYS960103	Number of contacts between side chains derived from 1168 x-ray protein structures
104	MIYS990106	Quasichemical energy of transfer of amino acids from water to the protein environment
105	LIWA970101	Modified version of the Miyazawa-Jernigan transfer energy
106	SIMK990102	Distance-dependent statistical potential (contacts within 5-7.5 Angstrooms)
107	SIMK990103	Distance-dependent statistical potential (contacts within 7.5-10 Angstrooms)
108	ZHAC000101	Environment-dependent residue contact energies (rows = helix, cols = helix)
109	ZHAC000102	Environment-dependent residue contact energies (rows = helix, cols = strand)
110	ZHAC000103	Environment-dependent residue contact energies (rows = helix, cols = coil)
111	ZHAC000104	Environment-dependent residue contact energies (rows = strand, cols = strand)
112	ZHAC000105	Environment-dependent residue contact energies (rows = strand, cols = coil)
113	ZHAC000106	Environment-dependent residue contact energies (rows = coil, cols = coil)
PSSM (6)
114	pssm_mut	PSSM Mutation
115	pssm_mut_weighted	Weighted PSSM
116	pssm_diff	Change in PSSM (Mutation – Wildtype)
117	pssm_weight_diff	Weighted change in PSSM (Mutation – Wildtype)
118	info_per_pos	Information per position
119	rel_weight_to_pseudo	Relative weight of gapless real matches to pseudocounts
	Conservation score (18)	Conservation score name
120	KABAT	KABAT
121	JORES	JORES
122	SCHNEIDER	SCHNEIDER
123	SHENKIN	SHENKIN
124	GERSTEIN	GERSTEIN
125	TAYLOR_GAPS	TAYLOR_GAPS
126	TAYLOR_NO_GAPS	TAYLOR_NO_GAPS
127	VELIBIL	VELIBIL
128	KARLIN	KARLIN
129	ARMON	ARMON
130	THOMPSON	THOMPSON
131	NOT_LANCET	NOT_LANCET
132	MIRNY	MIRNY
133	WILLIAMSON	WILLIAMSON
134	LANDGRAF	LANDGRAF
135	SANDER	SANDER
136	VALDAR	VALDAR
137	SMERFS	SMERFS
Full sequence (5)
138	aliphatic	Number of aliphatic residues in the protein
139	aromatic	Number of aromatic residues in the protein
140	Polar	Number of polar residues in the protein
141	Charged	Number of charged residues in the protein
142	keyres_pci	Number of key residues in the protein
Classification based on window length (10)
143	W7_aliphatic	Occurrence of aliphatic residues in window length of 7 residues
144	W7_aromatic	Occurrence of aromatic residues in window length of 7 residues
145	W7_polar	Occurrence of polar residues in window length of 7 residues
146	W7_charged	Occurrence of charged residues in window length of 7 residues
147	W7_keyres_pci	Occurrence of key residues in window length of 7 residues
148	W15_aliphatic	Occurrence of aliphatic residues in window length of 7 residues
149	W15_aromatic	Occurrence of aromatic residues in window length of 7 residues
150	W15_polar	Occurrence of polar residues in window length of 7 residues
151	W15_charged	Occurrence of charged residues in window length of 7 residues
152	W15_keyres_pci	Occurrence of key residues in window length of 7 residues
Structure-based features
Feature number	Property ID	Property Description
Residue depth (Bio.PDB) (1)
1	Residue_depth	Residue depth of the wildtype residue
HBPLUS (3)
2	donor	Number of donor in wildtype residue
3	acceptor	Number of acceptor in wildtype residue
4	combined	Number of donor and acceptor in wildtype residue
NACCESS (10)
5	All_atoms_ABS_diff	Absolute ASA difference of all atoms (Mut-Wt)
6	Total_Side_ABS_diff	Absolute ASA difference of side chain atoms (Mut-Wt)
7	Main_Chain_ABS_diff	Absolute ASA difference of main chain atoms (Mut-Wt)
8	Non_polar_ABS_diff	Absolute ASA difference of non-polar atoms (Mut-Wt)
9	All_polar_ABS_diff	Absolute ASA difference of polar atoms (Mut-Wt)
10	All_atoms_diff	Relative ASA difference of all atoms (Mut-Wt)
11	Total_Side_diff	Relative ASA difference of side chain atoms (Mut-Wt)
12	Main_Chain_diff	Relative ASA difference of main chain atoms (Mut-Wt)
13	Non_polar_diff	Relative ASA difference of non-polar atoms (Mut-Wt)
14	All_polar_diff	Relative ASA difference of polar atoms (Mut-Wt)
DSSP (3)
15	asa_wt_dssp	ASA of wildtype residue (DSSP)
16	asa_mut_dssp	ASA of mutant residue (DSSP)
17	asa_diff_dssp	ASA difference (Mut-WT) (DSSP)