메뉴 건너뛰기




Volumn 14, Issue SUPPL9, 2013, Pages

Solving the molecular distance geometry problem with inaccurate distance data

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL RESULTS; DISTANCE DATUM; ITERATIVE ALGORITHM; MAXIMUM CLIQUE; MOLECULAR DISTANCE GEOMETRY PROBLEM; NONLINEAR LEAST SQUARES; PROTEIN STRUCTURES; SOLUTION OF LINEAR SYSTEMS;

EID: 84887163959     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S9-S7     Document Type: Article
Times cited : (28)

References (26)
  • 2
    • 84988072837 scopus 로고
    • Linearized embedding: a new metric matrix algorithm for calculating molecular conformations subject to geometric constraints
    • Crippen GM. Linearized embedding: a new metric matrix algorithm for calculating molecular conformations subject to geometric constraints. Journal of Computational Chemistry 1989, 10(7):896-902.
    • (1989) Journal of Computational Chemistry , vol.10 , Issue.7 , pp. 896-902
    • Crippen, G.M.1
  • 6
    • 33847251002 scopus 로고    scopus 로고
    • An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data
    • Wu D, Wu Z. An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data. Journal of Global Optimization 2007, 37:661-673.
    • (2007) Journal of Global Optimization , vol.37 , pp. 661-673
    • Wu, D.1    Wu, Z.2
  • 7
    • 0031285908 scopus 로고    scopus 로고
    • Global continuation for distance geometry problems
    • Moré JJ, Wu Z. Global continuation for distance geometry problems. SIAM Journal on Optimization 1997, 7:814-836.
    • (1997) SIAM Journal on Optimization , vol.7 , pp. 814-836
    • Moré, J.J.1    Wu, Z.2
  • 8
    • 70350370784 scopus 로고    scopus 로고
    • A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation
    • 10.1007/s11538-009-9431-9, 19533250
    • Sit A, Wu Z, Yuan Y. A geometric buildup algorithm for the solution of the distance geometry problem using least-squares approximation. Bulletin of mathematical biology 2009, 71:1914-1933. 10.1007/s11538-009-9431-9, 19533250.
    • (2009) Bulletin of mathematical biology , vol.71 , pp. 1914-1933
    • Sit, A.1    Wu, Z.2    Yuan, Y.3
  • 9
    • 79955858230 scopus 로고    scopus 로고
    • Least-Squares Approximations in Geometric Buildup for Solving Distance Geometry Problems
    • Luo X, Wu Z. Least-Squares Approximations in Geometric Buildup for Solving Distance Geometry Problems. Journal of Optimization Theory and Applications 2011, 149:580-598.
    • (2011) Journal of Optimization Theory and Applications , vol.149 , pp. 580-598
    • Luo, X.1    Wu, Z.2
  • 11
    • 1342295659 scopus 로고    scopus 로고
    • A new algorithm for the maximum-weight clique problem
    • Östergård P. A new algorithm for the maximum-weight clique problem. Nordic J of Computing 2001, 8(4):424-436.
    • (2001) Nordic J of Computing , vol.8 , Issue.4 , pp. 424-436
    • Östergård, P.1
  • 12
    • 84867997005 scopus 로고    scopus 로고
    • A fast algorithm for the maximum clique problem
    • Östergård P. A fast algorithm for the maximum clique problem. Discrete Applied Mathematics 2002, 120:197-207.
    • (2002) Discrete Applied Mathematics , vol.120 , pp. 197-207
    • Östergård, P.1
  • 13
    • 84874426244 scopus 로고    scopus 로고
    • Cliquer User's Guide, Version 1.0, Communications Laboratory, Helsinki University of Technology, Espoo
    • Niskanen S, Östergård P. Cliquer User's Guide, Version 1.0, Communications Laboratory, Helsinki University of Technology, Espoo. Tech rep, Finland, Tech Rep 2003,
    • (2003) Tech rep, Finland, Tech Rep
    • Niskanen, S.1    Östergård, P.2
  • 14
    • 84887323262 scopus 로고    scopus 로고
    • CLIQUER: Routines for Clique Searching
    • CLIQUER: Routines for Clique Searching. , http://users.tkk.fi/pat/cliquer.html
  • 15
    • 84867997005 scopus 로고    scopus 로고
    • A fast algorithm for the maximum clique problem
    • Ostergard PRJ. A fast algorithm for the maximum clique problem. Discrete Appl Math 2002, 120:195-205.
    • (2002) Discrete Appl Math , vol.120 , pp. 195-205
    • Ostergard, P.R.J.1
  • 17
    • 55549138762 scopus 로고    scopus 로고
    • A Distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Conformation
    • Biswas P, Toh KC, Ye Y. A Distributed SDP Approach for Large-Scale Noisy Anchor-Free Graph Realization with Applications to Molecular Conformation. SIAM Journal on Scientific Computing 2008, 30:1251-1277.
    • (2008) SIAM Journal on Scientific Computing , vol.30 , pp. 1251-1277
    • Biswas, P.1    Toh, K.C.2    Ye, Y.3
  • 18
    • 80855147528 scopus 로고    scopus 로고
    • Hyperbolic smoothing and penalty techniques applied to molecular structure determination
    • Souza M, Xavier AE, Lavor C, Maculan N. Hyperbolic smoothing and penalty techniques applied to molecular structure determination. Operations Research Letters 2011, 39:461-465.
    • (2011) Operations Research Letters , vol.39 , pp. 461-465
    • Souza, M.1    Xavier, A.E.2    Lavor, C.3    Maculan, N.4
  • 19
    • 33749484908 scopus 로고    scopus 로고
    • Hyperbolic Penalty: A New Method for Nonlinear Programming with Inequalities
    • Xavier AE. Hyperbolic Penalty: A New Method for Nonlinear Programming with Inequalities. International Transactions in Operational Research 2001, 8:659-671.
    • (2001) International Transactions in Operational Research , vol.8 , pp. 659-671
    • Xavier, A.E.1
  • 20
    • 0003975791 scopus 로고
    • On The Limited Memory BFGS Method For Large Scale Optimization
    • Department of Electrical Engineering and Computer Science Northwestern University
    • Liu D, Nocedal. On The Limited Memory BFGS Method For Large Scale Optimization. Tech Rep NA-03 1988, Department of Electrical Engineering and Computer Science Northwestern University.
    • (1988) Tech Rep NA-03
    • Liu, D.1    Nocedal2
  • 21
    • 0004277557 scopus 로고    scopus 로고
    • Harwell Subroutine Library
    • Harwell Subroutine Library. , http://www.hsl.rl.ac.uk
  • 22
    • 0000935435 scopus 로고    scopus 로고
    • Distance Geometry Optimization for Protein Structures
    • Moré JJ, Wu Z. Distance Geometry Optimization for Protein Structures. Journal of Global Optimization 1999, 15:219-234.
    • (1999) Journal of Global Optimization , vol.15 , pp. 219-234
    • Moré, J.J.1    Wu, Z.2
  • 23
    • 84887170549 scopus 로고    scopus 로고
    • DGSOL: Distance Geometry Optimization Software
    • DGSOL: Distance Geometry Optimization Software. , http://www.mcs.anl.gov/~more/dgsol
  • 25
    • 0028334576 scopus 로고
    • Crystal structure of Y41H and Y41F mutants of gene V suggest possible protein-protein interactions in the GVP-SSDNA complex
    • 10.1021/bi00191a004, 8011642
    • Guan Y, Zhang H, Konings RNH, Hilbers CW, Terwilliger TC, Wang AHJ. Crystal structure of Y41H and Y41F mutants of gene V suggest possible protein-protein interactions in the GVP-SSDNA complex. Biochemistry 1994, 33:7768. 10.1021/bi00191a004, 8011642.
    • (1994) Biochemistry , vol.33 , pp. 7768
    • Guan, Y.1    Zhang, H.2    Konings, R.N.H.3    Hilbers, C.W.4    Terwilliger, T.C.5    Wang, A.H.J.6
  • 26
    • 0028325221 scopus 로고
    • Structure of the gene V protein of bacteriophage F1 determined by multi-wavelength X-ray diffraction on the selenomethionyl protein
    • 10.1073/pnas.91.6.2071, 43311, 8134350
    • Skinner M, Zhang H, Leschnitzer D, Guan Y, Bellamy H, Sweet R, Gray C, Konings R, Wang A, Terwilliger T. Structure of the gene V protein of bacteriophage F1 determined by multi-wavelength X-ray diffraction on the selenomethionyl protein. Proc Nat Acad Sci USA 1994, 91:2071. 10.1073/pnas.91.6.2071, 43311, 8134350.
    • (1994) Proc Nat Acad Sci USA , vol.91 , pp. 2071
    • Skinner, M.1    Zhang, H.2    Leschnitzer, D.3    Guan, Y.4    Bellamy, H.5    Sweet, R.6    Gray, C.7    Konings, R.8    Wang, A.9    Terwilliger, T.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.