-
1
-
-
0001094923
-
Carbonyl–carbonyl interactions can be competitive with hydrogen bonds
-
[1] Allen, F.H., Baalham, C.A., Lommerse, J.P.M., Raithby, P.R., Carbonyl–carbonyl interactions can be competitive with hydrogen bonds. Acta Crystallogr. B 54 (1998), 320–329.
-
(1998)
Acta Crystallogr. B
, vol.54
, pp. 320-329
-
-
Allen, F.H.1
Baalham, C.A.2
Lommerse, J.P.M.3
Raithby, P.R.4
-
2
-
-
34848842845
-
Geometry of nonbonded interactions involving planar groups in proteins
-
[2] Chakrabarti, P., Bhattacharyya, R., Geometry of nonbonded interactions involving planar groups in proteins. Prog. Biophys. Mol. Biol. 95 (2007), 83–137.
-
(2007)
Prog. Biophys. Mol. Biol.
, vol.95
, pp. 83-137
-
-
Chakrabarti, P.1
Bhattacharyya, R.2
-
3
-
-
65649095907
-
Halogen bonding—a novel interaction for rational drug design?
-
[3] Lu, Y., Shi, T., Wang, Y., Yang, H., Yan, X., Luo, X., et al. Halogen bonding—a novel interaction for rational drug design?. J. Med. Chem. 52 (2009), 2854–2862.
-
(2009)
J. Med. Chem.
, vol.52
, pp. 2854-2862
-
-
Lu, Y.1
Shi, T.2
Wang, Y.3
Yang, H.4
Yan, X.5
Luo, X.6
-
4
-
-
4243468938
-
The cation–pi interaction
-
[4] Ma, J.C., Dougherty, D.A., The cation–pi interaction. Chem. Rev. 97 (1997), 1303–1324.
-
(1997)
Chem. Rev.
, vol.97
, pp. 1303-1324
-
-
Ma, J.C.1
Dougherty, D.A.2
-
5
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
[5] McDonald, I.K., Thornton, J.M., Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994), 777–793.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
6
-
-
0032546782
-
Pi-stacking interactions. Alive and well in proteins
-
[6] McGaughey, G.B., Gagne, M., Rappe, A.K., Pi-stacking interactions. Alive and well in proteins. J. Biol. Chem. 273 (1998), 15,458–15,463.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 15458-15463
-
-
McGaughey, G.B.1
Gagne, M.2
Rappe, A.K.3
-
8
-
-
84940893103
-
Flexibility and small pockets at protein–protein interfaces: new insights into druggability
-
[8] Jubb, H., Blundell, T.L., Ascher, D.B., Flexibility and small pockets at protein–protein interfaces: new insights into druggability. Prog. Biophys. Mol. Biol. 119 (2015), 2–9.
-
(2015)
Prog. Biophys. Mol. Biol.
, vol.119
, pp. 2-9
-
-
Jubb, H.1
Blundell, T.L.2
Ascher, D.B.3
-
9
-
-
84892389578
-
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes
-
[9] Kasahara, K., Kinoshita, K., GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes. BMC Bioinformatics, 15, 2014, 12.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 12
-
-
Kasahara, K.1
Kinoshita, K.2
-
10
-
-
13044272912
-
Automated analysis of interatomic contacts in proteins
-
[10] Sobolev, V., Sorokine, A., Prilusky, J., Abola, E.E., Edelman, M., Automated analysis of interatomic contacts in proteins. Bioinformatics 15 (1999), 327–332.
-
(1999)
Bioinformatics
, vol.15
, pp. 327-332
-
-
Sobolev, V.1
Sorokine, A.2
Prilusky, J.3
Abola, E.E.4
Edelman, M.5
-
11
-
-
0031714858
-
JOY: protein sequence-structure representation and analysis
-
[11] Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson, M.S., Overington, J.P., JOY: protein sequence-structure representation and analysis. Bioinformatics 14 (1998), 617–623.
-
(1998)
Bioinformatics
, vol.14
, pp. 617-623
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.3
Johnson, M.S.4
Overington, J.P.5
-
12
-
-
0033614004
-
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
-
[12] Word, J.M., Lovell, S.C., Richardson, J.S., Richardson, D.C., Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J. Mol. Biol. 285 (1999), 1735–1747.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
13
-
-
84950255812
-
BiopLib and BiopTools—a C programming library and toolset for manipulating protein structure
-
[13] Porter, C.T., Martin, A.C., BiopLib and BiopTools—a C programming library and toolset for manipulating protein structure. Bioinformatics 31 (2015), 4017–4019.
-
(2015)
Bioinformatics
, vol.31
, pp. 4017-4019
-
-
Porter, C.T.1
Martin, A.C.2
-
14
-
-
80054911951
-
LigPlot +: multiple ligand–protein interaction diagrams for drug discovery
-
[14] Laskowski, R.A., Swindells, M.B., LigPlot +: multiple ligand–protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51 (2011), 2778–2786.
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2778-2786
-
-
Laskowski, R.A.1
Swindells, M.B.2
-
15
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
[15] Marcou, G., Rognan, D., Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J. Chem. Inf. Model. 47 (2007), 195–207.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
16
-
-
84891878468
-
PyPLIF: python-based protein-ligand interaction fingerprinting
-
[16] Radifar, M., Yuniarti, N., Istyastono, E.P., PyPLIF: python-based protein-ligand interaction fingerprinting. Bioinformation 9 (2013), 325–328.
-
(2013)
Bioinformation
, vol.9
, pp. 325-328
-
-
Radifar, M.1
Yuniarti, N.2
Istyastono, E.P.3
-
17
-
-
84979851890
-
PLIP: fully automated protein-ligand interaction profiler
-
[17] Salentin, S., Schreiber, S., Haupt, V.J., Adasme, M.F., Schroeder, M., PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res. 43 (2015), W443–W447.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. W443-W447
-
-
Salentin, S.1
Schreiber, S.2
Haupt, V.J.3
Adasme, M.F.4
Schroeder, M.5
-
18
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
-
[18] Berman, H., Henrick, K., Nakamura, H., Markley, J.L., The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35 (2007), D301–D303.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D301-D303
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
19
-
-
58149092163
-
CREDO: a protein–ligand interaction database for drug discovery
-
[19] Schreyer, A., Blundell, T., CREDO: a protein–ligand interaction database for drug discovery. Chem. Biol. Drug Des. 73 (2009), 157–167.
-
(2009)
Chem. Biol. Drug Des.
, vol.73
, pp. 157-167
-
-
Schreyer, A.1
Blundell, T.2
-
20
-
-
79960884702
-
Comprehensive, atomic-level characterization of structurally characterized protein–protein interactions: the PICCOLO database
-
[20] Bickerton, G.R., Higueruelo, A.P., Blundell, T.L., Comprehensive, atomic-level characterization of structurally characterized protein–protein interactions: the PICCOLO database. BMC Bioinformatics, 12, 2011, 313.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 313
-
-
Bickerton, G.R.1
Higueruelo, A.P.2
Blundell, T.L.3
-
21
-
-
70349756972
-
Atomic interactions and profile of small molecules disrupting protein–protein interfaces: the TIMBAL database
-
[21] Higueruelo, A.P., Schreyer, A., Bickerton, G.R., Pitt, W.R., Groom, C.R., Blundell, T.L., Atomic interactions and profile of small molecules disrupting protein–protein interfaces: the TIMBAL database. Chem. Biol. Drug Des. 74 (2009), 457–467.
-
(2009)
Chem. Biol. Drug Des.
, vol.74
, pp. 457-467
-
-
Higueruelo, A.P.1
Schreyer, A.2
Bickerton, G.R.3
Pitt, W.R.4
Groom, C.R.5
Blundell, T.L.6
-
22
-
-
66349098186
-
BIPA: a database for protein-nucleic acid interaction in 3D structures
-
[22] Lee, S., Blundell, T.L., BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinformatics 25 (2009), 1559–1560.
-
(2009)
Bioinformatics
, vol.25
, pp. 1559-1560
-
-
Lee, S.1
Blundell, T.L.2
-
23
-
-
84885906091
-
CREDO: a structural interactomics database for drug discovery
-
[23] Schreyer, A.M., Blundell, T.L., CREDO: a structural interactomics database for drug discovery. Database (Oxford), 2013, 2013, bat049.
-
(2013)
Database (Oxford)
, vol.2013
, pp. bat049
-
-
Schreyer, A.M.1
Blundell, T.L.2
-
24
-
-
65649092976
-
Biopython: freely available python tools for computational molecular biology and bioinformatics
-
[24] Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., et al. Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics 25 (2009), 1422–1423.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
Dalke, A.6
-
25
-
-
80053512597
-
Open Babel: an open chemical toolbox
-
[25] O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., Hutchison, G.R., Open Babel: an open chemical toolbox. J Cheminform., 3, 2011, 33.
-
(2011)
J Cheminform.
, vol.3
, pp. 33
-
-
O'Boyle, N.M.1
Banck, M.2
James, C.A.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.R.6
-
26
-
-
0346962971
-
Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein–ligand binding interactions
-
[26] Deng, Z., Chuaqui, C., Singh, J., Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein–ligand binding interactions. J. Med. Chem. 47 (2004), 337–344.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
27
-
-
0022450133
-
Amino-aromatic interactions in proteins
-
[27] Burley, S.K., Petsko, G.A., Amino-aromatic interactions in proteins. FEBS Lett. 203 (1986), 139–143.
-
(1986)
FEBS Lett.
, vol.203
, pp. 139-143
-
-
Burley, S.K.1
Petsko, G.A.2
-
28
-
-
66249145702
-
Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins
-
[28] Zhou, P., Tian, F., Lv, F., Shang, Z., Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins. Proteins 76 (2009), 151–163.
-
(2009)
Proteins
, vol.76
, pp. 151-163
-
-
Zhou, P.1
Tian, F.2
Lv, F.3
Shang, Z.4
-
29
-
-
84867427213
-
The methionine-aromatic motif plays a unique role in stabilizing protein structure
-
[29] Valley, C.C., Cembran, A., Perlmutter, J.D., Lewis, A.K., Labello, N.P., Gao, J., et al. The methionine-aromatic motif plays a unique role in stabilizing protein structure. J. Biol. Chem. 287 (2012), 34,979–34,991.
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 34979-34991
-
-
Valley, C.C.1
Cembran, A.2
Perlmutter, J.D.3
Lewis, A.K.4
Labello, N.P.5
Gao, J.6
-
30
-
-
84858641586
-
Strength of NH…S hydrogen bonds in methionine residues revealed by gas-phase IR/UV spectroscopy
-
[30] Biswal, H.S., Gloaguen, E., Loquais, Y., Tardivel, B., Mons, M., Strength of NH…S hydrogen bonds in methionine residues revealed by gas-phase IR/UV spectroscopy. J. Phys. Chem. Lett. 3 (2012), 755–759.
-
(2012)
J. Phys. Chem. Lett.
, vol.3
, pp. 755-759
-
-
Biswal, H.S.1
Gloaguen, E.2
Loquais, Y.3
Tardivel, B.4
Mons, M.5
-
31
-
-
84955485448
-
In silico functional dissection of saturation mutagenesis: interpreting the relationship between phenotypes and changes in protein stability, interactions and activity
-
[31] Pires, D.E., Chen, J., Blundell, T.L., Ascher, D.B., In silico functional dissection of saturation mutagenesis: interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Sci. Rep., 6, 2016, 19,848.
-
(2016)
Sci. Rep.
, vol.6
, pp. 19848
-
-
Pires, D.E.1
Chen, J.2
Blundell, T.L.3
Ascher, D.B.4
-
32
-
-
84951573472
-
Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy
-
[32] Nemethova, M., Radvanszky, J., Kadasi, L., Ascher, D.B., Pires, D.E., Blundell, T.L., et al. Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on ‘black bone disease’ in Italy. Eur. J. Hum. Genet. 24 (2016), 66–72.
-
(2016)
Eur. J. Hum. Genet.
, vol.24
, pp. 66-72
-
-
Nemethova, M.1
Radvanszky, J.2
Kadasi, L.3
Ascher, D.B.4
Pires, D.E.5
Blundell, T.L.6
-
33
-
-
84979835557
-
Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma
-
[33] Jafri, M., Wake, N.C., Ascher, D.B., Pires, D.E., Gentle, D., Morris, M.R., et al. Germline mutations in the CDKN2B tumor suppressor gene predispose to renal cell carcinoma. Cancer Discov. 5 (2015), 723–729.
-
(2015)
Cancer Discov.
, vol.5
, pp. 723-729
-
-
Jafri, M.1
Wake, N.C.2
Ascher, D.B.3
Pires, D.E.4
Gentle, D.5
Morris, M.R.6
-
34
-
-
84929366156
-
Analysis of HGD Gene mutations in patients with alkaptonuria from the United Kingdom: identification of novel mutations
-
[34] Usher, J.L., Ascher, D.B., Pires, D.E., Milan, A.M., Blundell, T.L., Ranganath, L.R., Analysis of HGD Gene mutations in patients with alkaptonuria from the United Kingdom: identification of novel mutations. JIMD Rep. 24 (2015), 3–11.
-
(2015)
JIMD Rep.
, vol.24
, pp. 3-11
-
-
Usher, J.L.1
Ascher, D.B.2
Pires, D.E.3
Milan, A.M.4
Blundell, T.L.5
Ranganath, L.R.6
-
35
-
-
84941044025
-
Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes
-
[35] Pires, D.E., Blundell, T.L., Ascher, D.B., Platinum: a database of experimentally measured effects of mutations on structurally defined protein–ligand complexes. Nucleic Acids Res. 43 (2015), D387–D391.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D387-D391
-
-
Pires, D.E.1
Blundell, T.L.2
Ascher, D.B.3
-
36
-
-
85007428022
-
Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance
-
[36] Phelan, J., Coll, F., McNerney, R., Ascher, D.B., Pires, D.E., Furnham, N., et al. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance. BMC Med., 14, 2016, 31.
-
(2016)
BMC Med.
, vol.14
, pp. 31
-
-
Phelan, J.1
Coll, F.2
McNerney, R.3
Ascher, D.B.4
Pires, D.E.5
Furnham, N.6
-
37
-
-
85018480535
-
Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis
-
[37] Park, Y., Pacitto, A., Bayliss, T., Cleghorn, L.A.T., Wang, Z., Hartman, T., et al. Essential but not vulnerable: indazole sulfonamides targeting inosine monophosphate dehydrogenase as potential leads against Mycobacterium tuberculosis. ACS Infect. Dis., 2016 (Epub ahead of print).
-
(2016)
ACS Infect. Dis.
-
-
Park, Y.1
Pacitto, A.2
Bayliss, T.3
Cleghorn, L.A.T.4
Wang, Z.5
Hartman, T.6
-
38
-
-
85018519349
-
The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis
-
[38] Singh, V., Donini, S., Pacitto, A., Sala, C., Hartkoorn, R.C., Dhar, N., et al. The inosine monophosphate dehydrogenase, GuaB2, is a vulnerable new bactericidal drug target for tuberculosis. ACS Infect. Dis., 2016 (Epub ahead of print).
-
(2016)
ACS Infect. Dis.
-
-
Singh, V.1
Donini, S.2
Pacitto, A.3
Sala, C.4
Hartkoorn, R.C.5
Dhar, N.6
|