메뉴 건너뛰기




Volumn 113, Issue 30, 2016, Pages E4286-E4293

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds

Author keywords

FFT; Manifold; Protein docking

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CORRELATIONAL STUDY; ENERGY; EVALUATION STUDY; FAST MANIFOLD FOURIER TRANSFORM; FEASIBILITY STUDY; FOURIER TRANSFORMATION; MOLECULAR DOCKING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN DOCKING; CHEMISTRY; FOURIER ANALYSIS; METABOLISM; PROCEDURES; REPRODUCIBILITY; ROTATION; THERMODYNAMICS;

EID: 84979518365     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1603929113     Document Type: Article
Times cited : (57)

References (36)
  • 1
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • Ritchie DW (2008) Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 9(1):1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , Issue.1 , pp. 1-15
    • Ritchie, D.W.1
  • 3
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein- protein docking
    • Vajda S, Kozakov D (2009) Convergence and combination of methods in protein- protein docking. Curr Opin Struct Biol 19(2):164-170.
    • (2009) Curr Opin Struct Biol , vol.19 , Issue.2 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 4
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJE (2002) Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12(1):38-35.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 35-38
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 5
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, et al. (1992) Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 89(6):2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.6 , pp. 2195-2199
    • Katchalski-Katzir, E.1
  • 6
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272(1): 106-120.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 7
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z (2003) ZDOCK: An initial-stage protein-docking algorithm. Proteins 52(1):80-87.
    • (2003) Proteins , vol.52 , Issue.1 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 8
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: An FFT-based protein docking program with pairwise potentials
    • Kozakov D, Brenke R, Comeau SR, Vajda S (2006) PIPER: An FFT-based protein docking program with pairwise potentials. Proteins 65(2):392-406.
    • (2006) Proteins , vol.65 , Issue.2 , pp. 392-406
    • Kozakov, D.1    Brenke, R.2    Comeau, S.R.3    Vajda, S.4
  • 9
    • 35449008122 scopus 로고    scopus 로고
    • Integrating statistical pair potentials into protein complex prediction
    • Mintseris J, et al. (2007) Integrating statistical pair potentials into protein complex prediction. Proteins 69(3):511-520.
    • (2007) Proteins , vol.69 , Issue.3 , pp. 511-520
    • Mintseris, J.1
  • 10
    • 0035040480 scopus 로고    scopus 로고
    • Protein docking using continuum electrostatics and geometric fit
    • Mandell JG, et al. (2001) Protein docking using continuum electrostatics and geometric fit. Protein Eng 14(2):105-113.
    • (2001) Protein Eng , vol.14 , Issue.2 , pp. 105-113
    • Mandell, J.G.1
  • 11
    • 0030248996 scopus 로고    scopus 로고
    • Low-resolution docking: Prediction of complexes for underdetermined structures
    • Vakser IA (1996) Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 39(3):455-464.
    • (1996) Biopolymers , vol.39 , Issue.3 , pp. 455-464
    • Vakser, I.A.1
  • 12
    • 77449134208 scopus 로고    scopus 로고
    • PIE-Efficient filters and coarse-grained potentials for unbound protein-protein docking
    • Ravikant DVS, Elber R (2010) PIE-Efficient filters and coarse-grained potentials for unbound protein-protein docking. Proteins 78(2):400-419.
    • (2010) Proteins , vol.78 , Issue.2 , pp. 400-419
    • Ravikant, D.V.S.1    Elber, R.2
  • 13
    • 0003711494 scopus 로고
    • ed Rossmann MG (Gordon and Breach, New York)
    • Crowther R (1972) The Molecular Replacement Method, ed Rossmann MG (Gordon and Breach, New York), pp 173-178.
    • (1972) The Molecular Replacement Method , pp. 173-178
    • Crowther, R.1
  • 14
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJ (2000) Protein docking using spherical polar Fourier correlations. Proteins 39(2):178-194.
    • (2000) Proteins , vol.39 , Issue.2 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 15
    • 50549092426 scopus 로고    scopus 로고
    • Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
    • Ritchie DW, Kozakov D, Vajda S (2008) Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 24(17):1865-1873.
    • (2008) Bioinformatics , vol.24 , Issue.17 , pp. 1865-1873
    • Ritchie, D.W.1    Kozakov, D.2    Vajda, S.3
  • 16
    • 0041566879 scopus 로고    scopus 로고
    • Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom
    • Kovacs JA, Chacón P, Cong Y, Metwally E, WriggersW(2003) Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom. Acta Crystallogr D Biol Crystallogr 59(Pt 8):1371-1376.
    • (2003) Acta Crystallogr D Biol Crystallogr , vol.59 , pp. 1371-1376
    • Kovacs, J.A.1    Chacón, P.2    Cong, Y.3    Metwally, E.4    Wriggers, W.5
  • 17
    • 70349882144 scopus 로고    scopus 로고
    • FRODOCK: A new approach for fast rotational protein-protein docking
    • Garzon JI, et al. (2009) FRODOCK: A new approach for fast rotational protein-protein docking. Bioinformatics 25(19):2544-2551.
    • (2009) Bioinformatics , vol.25 , Issue.19 , pp. 2544-2551
    • Garzon, J.I.1
  • 18
    • 77957242885 scopus 로고    scopus 로고
    • Ultra-fast FFT protein docking on graphics processors
    • Ritchie DW, Venkatraman V (2010) Ultra-fast FFT protein docking on graphics processors. Bioinformatics 26(19):2398-2405.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2398-2405
    • Ritchie, D.W.1    Venkatraman, V.2
  • 20
    • 84888295075 scopus 로고    scopus 로고
    • How good is automated protein docking?
    • Kozakov D, et al. (2013) How good is automated protein docking? Proteins 81(12): 2159-2166.
    • (2013) Proteins , vol.81 , Issue.12 , pp. 2159-2166
    • Kozakov, D.1
  • 21
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigidbody displacement and side-chain conformations
    • Gray JJ, et al. (2003) Protein-protein docking with simultaneous optimization of rigidbody displacement and side-chain conformations. J Mol Biol 331(1):281-299.
    • (2003) J Mol Biol , vol.331 , Issue.1 , pp. 281-299
    • Gray, J.J.1
  • 23
    • 0000273884 scopus 로고
    • Computing fourier transforms and convolutions on the 2-sphere
    • Driscoll J, Healy D (1994) Computing Fourier transforms and convolutions on the 2-sphere. Adv Appl Math 15(2):202-250.
    • (1994) Adv Appl Math , vol.15 , Issue.2 , pp. 202-250
    • Driscoll, J.1    Healy, D.2
  • 24
    • 26844527626 scopus 로고    scopus 로고
    • High-order analytic translation matrix elements for real-space sixdimensional polar Fourier correlations
    • Ritchie DW (2005) High-order analytic translation matrix elements for real-space sixdimensional polar Fourier correlations. J Appl Cryst 38(5):808-818.
    • (2005) J Appl Cryst , vol.38 , Issue.5 , pp. 808-818
    • Ritchie, D.W.1
  • 26
    • 20744449792 scopus 로고    scopus 로고
    • The design and implementation of FFTW3
    • Frigo M, Johnson SG (2005) The design and implementation of FFTW3. Proc IEEE 93(2): 216-231.
    • (2005) Proc IEEE , vol.93 , Issue.2 , pp. 216-231
    • Frigo, M.1    Johnson, S.G.2
  • 27
    • 58149152509 scopus 로고    scopus 로고
    • DARS (decoys as the reference state) potentials for protein-protein docking
    • Chuang GY, Kozakov D, Brenke R, Comeau SR, Vajda S (2008) DARS (Decoys As the Reference State) potentials for protein-protein docking. Biophys J 95(9):4217-4227.
    • (2008) Biophys J , vol.95 , Issue.9 , pp. 4217-4227
    • Chuang, G.Y.1    Kozakov, D.2    Brenke, R.3    Comeau, S.R.4    Vajda, S.5
  • 28
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Molec Biol 247(4):536-540.
    • (1995) J Molec Biol , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 29
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AMJJ (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125(7): 1731-1737.
    • (2003) J Am Chem Soc , vol.125 , Issue.7 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 30
    • 0030936560 scopus 로고    scopus 로고
    • Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N- Terminal domain of enzyme I of the Escherichia coli phosphotransferase system
    • Garrett DS, Seok YJ, Peterkofsky A, Clore GM, Gronenborn AM (1997) Identification by NMR of the binding surface for the histidine-containing phosphocarrier protein HPr on the N- Terminal domain of enzyme I of the Escherichia coli phosphotransferase system. Biochemistry 36(15):4393-4398.
    • (1997) Biochemistry , vol.36 , Issue.15 , pp. 4393-4398
    • Garrett, D.S.1    Seok, Y.J.2    Peterkofsky, A.3    Clore, G.M.4    Gronenborn, A.M.5
  • 31
    • 84890123384 scopus 로고    scopus 로고
    • Binding interface prediction by combining protein- protein docking results
    • Hwang H, Vreven T, Weng Z (2014) Binding interface prediction by combining protein- protein docking results. Proteins 82(1):57-66.
    • (2014) Proteins , vol.82 , Issue.1 , pp. 57-66
    • Hwang, H.1    Vreven, T.2    Weng, Z.3
  • 32
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernández-Recio J, Totrov M, Abagyan R (2004) Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 335(3):843-865.
    • (2004) J Mol Biol , vol.335 , Issue.3 , pp. 843-865
    • Fernández-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 33
    • 38049034590 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • Wiley, New York
    • Eswar N, et al. (2006) Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics (Wiley, New York), pp 561-5632.
    • (2006) Current Protocols in Bioinformatics , pp. 561-5632
    • Eswar, N.1
  • 35
    • 70350400724 scopus 로고    scopus 로고
    • A fast algorithm for nonequispaced Fourier transforms on the rotation group
    • Potts D, Prestin J, Vollrath A (2009) A fast algorithm for nonequispaced Fourier transforms on the rotation group. Numer Algorithms 52(3):355-384.
    • (2009) Numer Algorithms , vol.52 , Issue.3 , pp. 355-384
    • Potts, D.1    Prestin, J.2    Vollrath, A.3
  • 36
    • 84866363484 scopus 로고
    • On the use of symmetry in FFT computation
    • Rabiner L (1979) On the use of symmetry in FFT computation. IEEE Trans Acoust Speech Sig Proc 27(3):233-239.
    • (1979) IEEE Trans Acoust Speech Sig Proc , vol.27 , Issue.3 , pp. 233-239
    • Rabiner, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.