New constrained Langevin method: application to protein crystallographic refinement

被引：0

作者：

Pellegrini, Matteo ^{[1
]}

Larsen, Nick A. ^{[1
]}

Yeates, Todd O. ^{[1
]}

Gronbech-Jensen, Niels ^{[1
]}

机构：

[1] Univ of California, Los Angeles, United States

来源：

Physica A: Statistical Mechanics and its Applications | 1998年 / 261卷 / 1-2期

关键词：

Computer simulation - Conformations - Crystallography - Iterative methods - Lagrange multipliers - Linear equations - Molecular dynamics - Proteins;

D O I：

暂无

中图分类号：

学科分类号：

摘要：

We present an algorithm to perform Langevin simulations with constraints. The algorithm iteratively solves a set of linear equations to find the Lagrange multipliers that satisfy the constraints. We apply the algorithm to a polypeptide, and demonstrate that it is stable within a range of timesteps. The algorithm is then used to perform X-ray crystallographic refinement of proteins.

引用

页码：224 / 231

共 50 条

[21] APPLICATION OF MOLECULAR-DYNAMICS IN THE CRYSTALLOGRAPHIC REFINEMENT OF COLICIN-A
POSTMA, JPM
PARKER, MW
TSERNOGLOU, D
ACTA CRYSTALLOGRAPHICA SECTION A, 1989, 45 : 471 - 477
[22] TESTING THE METHOD OF CRYSTALLOGRAPHIC REFINEMENT USING MOLECULAR-DYNAMICS
FUJINAGA, M
GROS, P
VANGUNSTEREN, WF
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1989, 22 : 1 - 8
[23] MUMBO:: a protein-design approach to crystallographic model building and refinement
Stiebritz, Martin T.
Muller, Yves A.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2006, 62 : 648 - 658
[24] A new method of rigid-body refinement for protein crystal structures
Wei, Ding
Fan, Jiang
ACTA PHYSICA SINICA, 2011, 60 (04)
[25] Automating crystallographic structure solution and refinement of protein-ligand complexes
Echols, Nathaniel
Moriarty, Nigel W.
Klei, Herbert E.
Afonine, Pavel V.
Bunkoczi, Gabor
Headd, Jeffrey J.
McCoy, Airlie J.
Oeffner, Robert D.
Read, Randy J.
Terwilliger, Thomas C.
Adams, Paul D.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2014, 70 : 144 - 154
[26] Constrained groove pressing and its application to grain refinement of aluminum
Shin, DH
Park, JJ
Kim, YS
Park, KT
MATERIALS SCIENCE AND ENGINEERING A-STRUCTURAL MATERIALS PROPERTIES MICROSTRUCTURE AND PROCESSING, 2002, 328 (1-2): : 98 - 103
[27] CRYSTALLOGRAPHIC TEXTURE AND GRAIN REFINEMENT IN THE CuCr ALLOY DEFORMED BY SPD METHOD
Urbanczyk-Gucwa, A.
Brzezinska, A.
Adamczyk-Cieslak, B.
Rodak, K.
ARCHIVES OF METALLURGY AND MATERIALS, 2019, 64 (04) : 1563 - 1568
[28] ResDe: a new tool for visual definition of distance restraints for crystallographic refinement
Hintze, Bradley J.
Johnson, Sean J.
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 2010, 43 : 1540 - 1542
[29] ON A REFINEMENT OF THE CONVERGENCE ANALYSIS FOR THE NEW EXACT PENALTY FUNCTION METHOD FOR CONTINUOUS INEQUALITY CONSTRAINED OPTIMIZATION PROBLEM
Yu, Changjun
Teo, Kok Lay
Zhang, Liansheng
Bai, Yanqin
JOURNAL OF INDUSTRIAL AND MANAGEMENT OPTIMIZATION, 2012, 8 (02) : 485 - 491
[30] Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration
Fenn, Timothy D.
Schnieders, Michael J.
Mustyakimov, Marat
Wu, Chuanjie
Langan, Paul
Pande, Vijay S.
Brunger, Axel T.
STRUCTURE, 2011, 19 (04) : 523 - 533

← 1 2 3 4 5 →