Binding cavities and druggability of intrinsically disordered proteins

Protein Science

Volumn 24, Issue 5, 2015, Pages 688-705

  Zhang, Yugang ^a,b   Cao, Huaiqing ^a,b   Liu, Zhirong ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

drug design; drug target; druggability; intrinsically disordered protein; ligandability; molecular recognition; pE DB

Indexed keywords

26S PROTEASOME COMPLEX SUBUNIT DSS1; ANTI SIGMA FACTOR FLGM; APROTININ; ATP SYNTHASE COUPLING FACTOR 6; ATRIAL NATRIURETIC FACTOR; BCL2 ANTAGONIST OF CELL DEATH; CALSEQUESTRIN 1; CORE PROTEIN P19; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DYNEIN INTERMEDIATE CHAIN; FACT COMPLEX SUBUNIT SSRP1; GIBBERELLIN RECEPTOR GID1A; HIGH MOBILITY GROUP PROTEIN; HISTONE BINDING PROTEIN N1; HISTONE H1; HOMEOBOX PROTEIN NKX 2.1; INTRINSICALLY DISORDERED PROTEIN; LAMIN A; ONCOMODULIN; PARATHYROID HORMONE; PROTEIN; PROTEIN AF9; PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 12A; PROTEIN UMUD; SERINE THREONINE PROTEIN 5; TRANSCRIPTION FACTOR 7 LIKE 2; TRANSCRIPTION FACTOR P65; TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1; UNCLASSIFIED DRUG; YES ASSOCIATED PROTEIN; LIGAND; PROTEIN BINDING;

ARTICLE; CONFORMATION; CONTROLLED STUDY; DRUG DESIGN; GEOMETRY; LIGAND BINDING; PRIORITY JOURNAL; SURFACE AREA; CHEMISTRY; HUMAN; PROTEIN CONFORMATION; PROTEIN DATABASE; THERMODYNAMICS;

DATABASES, PROTEIN; DRUG DESIGN; HUMANS; INTRINSICALLY DISORDERED PROTEINS; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 84956724255     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2641     Document Type: Article

References (94)

1. Uversky VN, (2013) A decade and a half of protein intrinsic disorder: biology still waits for physics. Protein Sci 22: 693-724.
2. Huang YQ, Liu ZR, (2010) Intrinsically disordered proteins: the new sequence-structure-function relations. Acta Phys Chim Sin 26: 2061-2072.
3. Dunker AK, Lawson JD, Brown CJ, Williams RM, Romero P, Oh JS, Oldfield CJ, Campen AM, Ratliff CR, Hipps KW, Ausio J, Nissen MS, Reeves R, Kang CH, Kissinger CR, Bailey RW, Griswold MD, Chiu M, Garner EC, Obradovic Z, (2001) Intrinsically disordered protein. J Mol Graph Model 19: 26-59.
4. Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J Mol Biol 293: 321-331.
5. Iakoucheva LM, Brown CJ, Lawson JD, Obradovic Z, Dunker AK, (2002) Intrinsic disorder in cell-signaling and cancer-associated proteins. J Mol Biol 323: 573-584.
6. Cheng Y, LeGall T, Oldfield CJ, Mueller JP, Van YYJ, Romero P, Cortese MS, Uversky VN, Dunker AK, (2006) Rational drug design via intrinsically disordered protein. Trends Biotechnol 24: 435-442.
7. Metallo SJ, (2010) Intrinsically disordered proteins are potential drug targets. Curr Opin Chem Biol 14: 481-488.
8. Xie HB, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN, Obradovic Z, (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6: 1882-1898.
9. Midic U, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN, (2009) Protein disorder in the human diseasome: unfoldomics of human genetic diseases. BMC Genomics 10: 12.
10. Babu MM, van der Lee R, de Groot NS, Gsponer J, (2011) Intrinsically disordered proteins: regulation and disease. Curr Opin Struct Biol 21: 432-440.
11. Mendoza-Espinosa P, Garcia-Gonzalez V, Moreno A, Castillo R, Mas-Oliva J, (2009) Disorder-to-order conformational transitions in protein structure and its relationship to disease. Mol Cell Biochem 330: 105-120.
12. Cheng YG, LeGall T, Oldfield CJ, Dunker AK, Uversky VN, (2006) Abundance of intrinsic disorder in protein associated with cardiovascular disease. Biochemistry 45: 10448-10460.
13. 2 concept. Annu Rev Biophys 37: 215-246.
14. Dunker AK, Uversky VN, (2010) Drugs for 'protein clouds': targeting intrinsically disordered transcription factors. Curr Opin Pharmacol 10: 782-788.
15. Wang JH, Cao ZX, Zhao LL, Li SQ, (2011) Novel strategies for drug discovery based on intrinsically disordered proteins (IDPs). Int J Mol Sci 12: 3205-3219.
16. Chen CYC, Tou WL, (2013) How to design a drug for the disordered proteins. Drug Discov Today 18: 910-915.
17. Yuan YX, Pei JF, Lai LH, (2011) LigBuilder 2: a practical de novo drug design approach. J Chem Inf Model 51: 1083-1091.
18. Jin F, Yu C, Lai LH, Liu ZR, (2013) Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PLoS Comput Biol 9: e1003249.
19. Chene P, (2004) Inhibition of the p53-MDM2 interaction: targeting a protein-protein interface. Mol Cancer Res 2: 20-28.
20. Erkizan HV, Kong YL, Merchant M, Schlottmann S, Barber-Rotenberg JS, Yuan LS, Abaan OD, Chou TH, Dakshanamurthy S, Brown ML, Uren A, Toretsky JA, (2009) A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma. Nat Med 15: 750-757.
21. Hammoudeh DI, Follis AV, Prochownik EV, Metallo SJ, (2009) Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. J Am Chem Soc 131: 7390-7401.
22. Srinivasan RS, Nesbit JB, Marrero L, Erfurth F, LaRussa VF, Hemenway CS, (2004) The synthetic peptide PFWT disrupts AF4-AF9 protein complexes and induces apoptosis in t(4;11) leukemia cells. Leukemia 18: 1364-1372.
23. Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Munch J, Baker D, Eisenberg D, (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature 475: 96-100.
24. Yuzwa SA, Macauley MS, Heinonen JE, Shan XY, Dennis RJ, He YA, Whitworth GE, Stubbs KA, McEachern EJ, Davies GJ, Vocadlo DJ, (2008) A potent mechanism-inspired O-GlcNAcase inhibitor that blocks phosphorylation of tau in vivo. Nat Chem Biol 4: 483-490.
25. Yuan YX, Pei JF, Lai LH, (2013) Binding site detection and druggability prediction of protein targets for structure-based drug design. Curr Pharm Des 19: 2326-2333.
26. Huang YQ, Liu ZR, (2009) Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J Mol Biol 393: 1143-1159.
27. Gunasekaran K, Tsai CJ, Kumar S, Zanuy D, Nussinov R, (2003) Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci 28: 81-85.
28. Meszaros B, Tompa P, Simon I, Dosztanyi Z, (2007) Molecular principles of the interactions of disordered proteins. J Mol Biol 372: 549-561.
29. Huang YQ, Liu ZR, (2010) Smoothing molecular interactions: the "kinetic buffer" effect of intrinsically disordered proteins. Proteins 78: 3251-3259.
30. Varadi M, Kosol S, Lebrun P, Valentini E, Blackledge M, Dunker AK, Felli IC, Forman-Kay JD, Kriwacki RW, Pierattelli R, Sussman J, Svergun DI, Uversky VN, Vendruscolo M, Wishart D, Wright PE, Tompa P, (2014) pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins. Nucleic Acids Res 42: D326-D335.
31. Laurie ATR, Jackson RM, (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916.
32. Liu ZR, Huang YQ, (2014) Advantages of proteins being disordered. Protein Sci 23: 539-550.
33. Knott M, Best RB, (2012) A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PLoS Comput Biol 8: e1002605.
34. Uversky VN, (2013) Unusual biophysics of intrinsically disordered proteins. Biochim Biophys Acta 1834: 932-951.
35. Song JH, Ng SC, Tompa P, Lee KAW, Chan HS, (2013) Polycation-pi interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family. PLoS Comput Biol 9: e1003239.
36. Huang YQ, Liu ZR, (2013) Do intrinsically disordered proteins possess high specificity in protein-protein interactions? Chem-Eur J 19: 4462-4467.
37. Fuxreiter M, Simon I, Friedrich P, Tompa P, (2004) Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 338: 1015-1026.
38. Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN, (2006) Analysis of molecular recognition features (MoRFs). J Mol Biol 362: 1043-1059.
39. Disfani FM, Hsu WL, Mizianty MJ, Oldfield CJ, Xue B, Dunker AK, Uversky VN, Kurgan L, (2012) MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins. Bioinformatics 28: I75-I83.
40. Vassilev LT, Vu BT, Graves B, Carvajal D, Podlaski F, Filipovic Z, Kong N, Kammlott U, Lukacs C, Klein C, Fotouhi N, Liu EA, (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303: 844-848.
41. Yu X, Narayanan S, Vazquez A, Carpizo DR, (2014) Small molecule compounds targeting the p53 pathway: are we finally making progress? Apoptosis 19: 1055-1068.
42. Tovar C, Rosinski J, Filipovic Z, Higgins B, Kolinsky K, Hilton H, Zhao XL, Vu BT, Qing WG, Packman K, Myklebost O, Heimbrook DC, Vassilev LT, (2006) Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. Proc Natl Acad Sci USA 103: 1888-1893.
43. Berg T, Cohen SB, Desharnais J, Sonderegger C, Maslyar DJ, Goldberg J, Boger DL, Vogt PK, (2002) Small-molecule antagonists of Myc/Max dimerization inhibit Myc-induced transformation of chicken embryo fibroblasts. Proc Natl Acad Sci USA 99: 3830-3835.
44. Shi J, Stover JS, Whitby LR, Vogt PK, Boger DL, (2009) Small molecule inhibitors of Myc/Max dimerization and Myc-induced cell transformation. Bioorg Med Chem Lett 19: 6038-6041.
45. Yin XY, Giap C, Lazo JS, Prochownik EV, (2003) Low molecular weight inhibitors of Myc-Max interaction and function. Oncogene 22: 6151-6159.
46. Zirath H, Frenzel A, Oliynyk G, Segerstrom L, Westermark UK, Larsson K, Persson MM, Hultenby K, Lehtio J, Einvik C, Pahlman S, Kogner P, Jakobsson PJ, Henriksson MA, (2013) MYC inhibition induces metabolic changes leading to accumulation of lipid droplets in tumor cells. Proc Natl Acad Sci USA 110: 10258-10263.
47. Fletcher S, Prochownik EV, (in press) Small-molecule inhibitors of the Myc oncoprotein. Biochim Biophys Acta.
48. Hong SH, Youbi SE, Hong SP, Kallakury B, Monroe P, Erkizan HV, Barber-Rotenberg JS, Houghton P, Uren A, Toretsky JA, (2014) Pharmacokinetic modeling optimizes inhibition of the 'undruggable' EWS-FLI1 transcription factor in Ewing Sarcoma. Oncotarget 5: 338-350.
49. Palermo CM, Bennett CA, Winters AC, Hemenway CS, (2008) The AF4-mimetic peptide, PFWT, induces necrotic cell death in MV4-11 leukemia cells. Leuk Res 32: 633-642.
50. Bennett CA, Winters AC, Barretto NN, Hemenway CS, (2009) Molecular targeting of MLL-rearranged leukemia cell lines with the synthetic peptide PFWT synergistically enhances the cytotoxic effect of established chemotherapeutic agents. Leuk Res 33: 937-947.
51. Watson VG, Drake KM, Peng Y, Napper AD, (2013) Development of a high-throughput screening-compatible assay for the discovery of inhibitors of the AF4-AF9 interaction using AalphaScreen technology. Assay Drug Dev Technol 11: 253-268.
52. Krishnan N, Koveal D, Miller DH, Xue B, Akshinthala SD, Kragelj J, Jensen MR, Gauss CM, Page R, Blackledge M, Muthuswamy SK, Peti W, Tonks NK, (2014) Targeting the disordered C terminus of PTP1B with an allosteric inhibitor. Nat Chem Biol 10: 558-566.
53. Fokkens M, Schrader T, Klarner FG, (2005) A molecular tweezer for lysine and arginine. J Am Chem Soc 127: 14415-14421.
54. Prabhudesai S, Sinha S, Attar A, Kotagiri A, Fitzmaurice AG, Lakshmanan R, Ivanova MI, Loo JA, Klarner FG, Schrader T, Stahl M, Bitan G, Bronstein JM, (2012) A novel "molecular tweezer" inhibitor of alpha-Synuclein neurotoxicity in vitro and in vivo. Neurotherapeutics 9: 464-476.
55. Sinha S, Lopes DHJ, Du ZM, Pang ES, Shanmugam A, Lomakin A, Talbiersky P, Tennstaedt A, McDaniel K, Bakshi R, Kuo PY, Ehrmann M, Benedek GB, Loo JA, Klarner FG, Schrader T, Wang CY, Bitan G, (2011) Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins. J Am Chem Soc 133: 16958-16969.
56. Toth G, Gardai SJ, Zago W, Bertoncini CW, Cremades N, Roy SL, Tambe MA, Rochet JC, Galvagnion C, Skibinski G, Finkbeiner S, Bova M, Regnstrom K, Chiou SS, Johnston J, Callaway K, Anderson JP, Jobling MF, Buell AK, Yednock TA, Knowles TPJ, Vendruscolo M, Christodoulou J, Dobson CM, Schenk D, McConlogue L, (2014) Targeting the intrinsically disordered structural ensemble of alpha-Synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease. PLoS One 9: 87133.
57. Tompa P, (2011) Unstructural biology coming of age. Curr Opin Struct Biol 21: 419-425.
58. Cuchillo R, Michel J, (2012) Mechanisms of small-molecule binding to intrinsically disordered proteins. Biochem Soc Trans 40: 1004-1008.
59. Uversky VN, (2012) Intrinsically disordered proteins and novel strategies for drug discovery. Expert Opin Drug Discov 7: 475-488.
60. Joerger AC, Fersht AR, (2008) Structural biology of the tumor suppressor p53. Annu Rev Biochem 77: 557-582.
61. Li ZY, Ni M, Li JK, Zhang YP, Ouyang Q, Tang C, (2011) Decision making of the p53 network: Death by integration. J Theor Biol 271: 205-211.
62. Huang YQ, Liu ZR, (2011) Anchoring intrinsically disordered proteins to multiple targets: Lessons from N-terminus of the p53 protein. Int J Mol Sci 12: 1410-1430.
63. Leach BI, Kuntimaddi A, Schmidt CR, Cierpicki T, Johnson SA, Bushweller JH, (2013) Leukemia fusion target AF9 is an intrinsically disordered transcriptional regulator that recruits multiple partners via coupled folding and binding. Structure 21: 176-183.
64. Hegyi H, Buday L, Tompa P, (2009) Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PLoS Comput Biol 5: 1000552.
65. Johnson TO, Ermolieff J, Jirousek MR, (2002) Protein tyrosine phosphatase 1B inhibitors for diabetes. Nat Rev Drug Discov 1: 696-709.
66. Tompa P, (2014) Multisteric regulation by structural disorder in modular signaling proteins: an extension of the concept of allostery. Chem Rev 114: 6715-6732.
67. Jin F, Liu ZR, (2013) Inherent relationships among different biophysical prediction methods for intrinsically disordered proteins. Biophys J 104: 488-495.
68. Zhu M, De Simone A, Schenk D, Toth G, Dobson CM, Vendruscolo M, (2013) Identification of small-molecule binding pockets in the soluble monomeric form of the A beta 42 peptide. J Chem Phys 139: 035101.
69. Hsu SY, Kaipia A, Zhu L, Hsueh AJW, (1997) Interference of BAD (Bcl-xL/Bcl-2-associated death promoter)-induced apoptosis in mammalian cells by 14-3-3 isoforms and P11. Mol Endocrinol 11: 1858-1867.
70. Li Z, Zhao B, Wang P, Chen F, Dong ZH, Yang HR, Guan KL, Xu YH, (2010) Structural insights into the YAP and TEAD complex. Genes Dev 24: 235-240.
71. Wang SR, Trumble WR, Liao H, Wesson CR, Dunker AK, Kang CH, (1998) Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum. Nat Struct Biol 5: 476-483.
72. Jin L, Briggs SL, Chandrasekhar S, Chirgadze NY, Clawson DK, Schevitz RW, Smiley DL, Tashjian AH, Zhang FM, (2000) Crystal structure of human parathyroid hormone 1-34 at 0.9-angstrom resolution. J Biol Chem 275: 27238-27244.
73. DiGiammarino EL, Filippov I, Weber JD, Bothner B, Kriwacki RW, (2001) Solution structure of the p53 regulatory domain of the p19(Arf) tumor suppressor protein. Biochemistry 40: 2379-2386.
74. Hayes PL, Lytle BL, Volkman BF, Peterson FC, (2008) The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured protein. Protein Sci 17: 571-576.
75. Furst J, Schedlbauer A, Gandini R, Garavaglia ML, Saino S, Gschwentner M, Sarg B, Lindner H, Jakab M, Ritter M, Bazzini C, Botta G, Meyer G, Kontaxis G, Tilly BC, Konrat R, Paulmichl M, (2005) ICln(159) folds into a pleckstrin homology domain-like structure. J Biol Chem 280: 31276-31282.
76. Kobashigawa Y, Sakai M, Naito M, Yokochi M, Kumeta H, Makino Y, Ogura K, Tanaka S, Inagaki F, (2007) Structural basis for the transforming activity of human cancer-related signaling adaptor protein CRK. Nat Struct Mol Biol 14: 503-510.
77. Ellena JF, Liang BY, Wiktor M, Stein A, Cafiso DS, Jahn R, Tamm LK, (2009) Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation. Proc Natl Acad Sci USA 106: 20306-20311.
78. Sivakolundu SG, Bashford D, Kriwacki RW, (2005) Disordered p27(Kip1) exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation. J Mol Biol 353: 1118-1128.
79. De Biasio A, de Opakua AI, Cordeiro TN, Villate M, Merino N, Sibille N, Lelli M, Diercks T, Bernado P, Blanco FJ, (2014) p15(PAF) is an intrinsically disordered protein with nonrandom structural preferences at sites of interaction with other proteins. Biophys J 106: 865-874.
80. Lee VMY, Goedert M, Trojanowski JQ, (2001) Neurodegenerative tauopathies. Annu Rev Neurosci 24: 1121-1159.
81. Crawford M, Brawner E, Batte K, Yu L, Hunter MG, Otterson GA, Nuovo G, Marsh CB, Nana-Sinkam SP, (2008) MicroRNA-126 inhibits invasion in non-small cell lung carcinoma cell lines. Biochem Biophys Res Commun 373: 607-612.
82. Yu PW, Huang B, Shen M, Lau C, Chan E, Michel J, Xiong Y, Payan DG, Luo Y, (2001) p15(PAF), a novel PCNA associated factor with increased expression in tumor tissues. Oncogene 20: 484-489.
83. Borriello A, Bencivenga D, Criscuolo M, Caldarelli I, Cucciolla V, Tramontano A, Borgia A, Spina A, Oliva A, Naviglio S, Della Ragione F, (2011) Targeting p27(Kip1) protein: its relevance in the therapy of human cancer. Expert Opin Ther Targets 15: 677-693.
84. Wang Q, Qi YF, Yin N, Lai LH, (2014) Discovery of novel allosteric effectors based on the predicted allosteric sites for Escherichia coli D-3-phosphoglycerate dehydrogenase. PLoS One 9: e94829.
85. Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F, (2013) Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling. Cancer Cell 23: 489-501.
86. Walters BJ, Lin WW, Diao SY, Brimble M, Iconaru LI, Dearman J, Goktug A, Chen TS, Zuo J, (2014) High-throughput screening reveals alsterpaullone, 2-cyanoethyl as a potent p27(Kip1) transcriptional inhibitor. PLoS One 9: e91173.
87. Bhattacherjee A, Wallin S, (2013) Exploring protein-peptide binding specificity through computational peptide screening. PLoS Comput Biol 9: e1003277.
88. Zhou HX, (2012) Intrinsic disorder: signaling via highly specific but short-lived association. Trends Biochem Sci 37: 43-48.
89. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK, (2007) DisProt: the database of disordered proteins. Nucleic Acids Res 35: D786-D793.
90. Berman H, Henrick K, Nakamura H, Markley JL, (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35: D301-D303.
91. Wang RX, Fang XL, Lu YP, Wang SM, (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47: 2977-2980.
92. Hendlich M, Rippmann F, Barnickel G, (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15: 359-363.
93. Laskowski RA, (1995) SURFNET-a program for visualizing molecular-surfaces, cavities, and intermolecular interactions. J Mol Graph 13: 323-330.
94. Brady GP, Stouten PFW, (2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput-Aided Mol Des 14: 383-401.