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The Use of Refmac Crystallographic Refinement Program for Detection of Alternative Conformations in Biological Macromolecules
Использование программы кристаллографического уточнения Refmac в процессе выявления альтернативных конформаций в биологических макромолекулах

О.В. Соболев, O.V. Sobolev
2012 Математическая биология и биоинформатика  
The construction of databases with atomic shifts, their analysis and the development of automatic decision-making procedures for detection of alternative conformations with the use of popular refinement  ...  The analysis also showed that probability distributions of atomic shifts appear to depend on the program used for refinement, so the decision making procedures should be adapted to the refinement program  ...  RESULTS AND DUSCUSSION Diagrams of atomic shifts Atomic mobility in unrestrained refinement All atoms in the databases can be divided in two types, namely SC-atoms and AC-atoms.  ... 
doi:10.17537/2012.7.692 fatcat:po33ayhmt5fbjjl3ndb625xinq

Automated and Modular Refinement Reasoning for Concurrent Programs [chapter]

Chris Hawblitzel, Erez Petrank, Shaz Qadeer, Serdar Tasiran
2015 Lecture Notes in Computer Science  
Atomic actions in a high-level description are refined to fine-grain and optimized lower-level implementations.  ...  Modular specifications and proof annotations, such as location invariants and procedure pre-and post-conditions, are specified separately, independently at each level in terms of the variables visible  ...  A subset of the atomic actions may be refined by new procedures and a new program is obtained by replacing the invocation of an atomic action by a call to the corresponding procedure refining the action  ... 
doi:10.1007/978-3-319-21668-3_26 fatcat:n2eslalhbzfbtbeplhbj65pwju

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

Thomas C. Terwilliger, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Nigel W. Moriarty, Paul D. Adams, Randy J. Read, Peter H. Zwart, Li-Wei Hung
2008 Acta Crystallographica Section D: Biological Crystallography  
A procedure for carrying out iterative model-building, density modification and refinement is presented in which the density in an OMIT region is essentially unbiased by an atomic model.  ...  The procedure may have applications in the validation of specific features in atomic models as well as in overall model validation.  ...  and refinement need to keep track of which atoms are in the OMIT and border regions.  ... 
doi:10.1107/s0907444908004319 pmid:18453687 pmcid:PMC2424225 fatcat:7xsb5y2cbjemdft2c4iaapmsqy

Better data – proper redundancy

M. Wedel, H. Borrmann
2012 Acta Crystallographica Section A Foundations of Crystallography  
The procedure is based on the observation that single-conformation and alternative-conformations residues have different mobility in unrestrained refinement.  ...  To get these hints in a routine way we suggest two procedures that analyze amplitudes of atomic shifts resulted from several cycles of unrestrained refinement.  ...  The procedure is based on the observation that single-conformation and alternative-conformations residues have different mobility in unrestrained refinement.  ... 
doi:10.1107/s010876731209842x fatcat:hddsjin4fffbngvkyrwc7gprvq

Layered Concurrent Programs [chapter]

Bernhard Kragl, Shaz Qadeer
2018 Lecture Notes in Computer Science  
These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls.  ...  We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs.  ...  Henzinger, Viktor Toman, and James R. Wilcox for comments that improved this paper.  ... 
doi:10.1007/978-3-319-96145-3_5 fatcat:coe4wsx6lbc53fnbszh5333csy

Detection of alternative conformations:Shift_plotandAC_predictionprograms

Oleg V. Sobolev
2013 Journal of Applied Crystallography  
procedures based on atomic shift magnitudes in unrestrained refinement to highlight the specific residues that are likely to harbour alternative conformations and that hence require checkingviaelectron  ...  Increased mobility of poorly ordered atoms compared to well ordered ones in unrestrained refinement was adopted as the basis for the development of a method for predicting alternative conformations.  ...  Figs. 6 and 7 were prepared using PyMOL (DeLano, 2002) . This work was supported by RFBR grant 12-04-31096.  ... 
doi:10.1107/s0021889812052065 fatcat:mocqp7lzhfhqhoe2ig3372f2ze

Atomic model building and refinement into high-resolution cryo-EM maps

Bruno Klaholz, S. Kundhavai Natchiar, Alexander Myasnikov, Hanna Kratzat, Isabelle Hazemann, Bruno Klaholz
2017 Protocol Exchange  
Here we present a generally applicable protocol for atomic model building and refinement into high-resolution cryo-EM maps, which in addition includes the refinement of nucleotides and amino acids with  ...  The interpretation of high-resolution cryo electron microscopy (cryo-EM) maps relies on the creation of precise atomic models that help analyzing the detailed interactions within a macromolecular complex  ...  Acknowledgements We thank Jonathan Michalon, Remy Fritz and Romaric David for IT support.  ... 
doi:10.1038/protex.2017.122 fatcat:v5oxfrmasvdpvbhhlem2ncb4lu

A method for refinement of partially interpreted protein structures including a procedure for scaling between a model and an electron-density map

T. N. Bhat, D. M. Blow
1983 Acta Crystallographica Section A Foundations of Crystallography  
A method for the structure-factor least-squares refinement of a poor and incomplete atomic model of a protein molecule is suggested.  ...  an R-factor search procedure.  ...  desirable to introduce a procedure for refinement of the atomic model (which is likely to be tentative and incomplete) within each cycle of the procedure.  ... 
doi:10.1107/s0108767383000264 fatcat:pcwzhzklqvc7rdxhapwlfwr5wi

Introducing iterative X-ray wavefunction refinement

Rumpa Pal, Emanuel Hupf, Dylan Jayatilaka, Simon Grabowsky
2017 Acta Crystallographica Section A: Foundations and Advances  
Hirshfeld atom refinement (HAR)[1] is a structural refinement method of single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular  ...  The original HAR has been extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares  ...  Hirshfeld atom refinement (HAR)[1] is a structural refinement method of single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular  ... 
doi:10.1107/s2053273317088726 fatcat:yqnziotikzbjtcua4x3ktf25im

A Gauss–Seidel least-squares refinement procedure with rigid-group and parameter restraint capabilities

L. G. Hoard, C. E. Nordman
1979 Acta Crystallographica Section A  
A fast Gauss-Seidel least-squares procedure (FGLS) has been developed for crystallographic refinement of atom parameters in large asymmetric units.  ...  The procedure combines the minimum matrix requirements and the rapid convergence of the Gauss-Seidel algorithm with rigid-group constraint and subsidiary parameter elastic restraint capabilities.  ...  The outermost loop is over the atoms, where the pointers IAT1 and IAT2 indicate the first and last atoms, respectively, to be refined in the list of unique atoms.  ... 
doi:10.1107/s0567739479002229 fatcat:chyhmjvrd5fuffey5ttzc22yme

Prediction of alternative and disordered residues by unrestrained refinement

Oleg V. Sobolev, Vladimir Y. Lunin
2013 Acta Crystallographica Section A Foundations of Crystallography  
Unrestrained reciprocal space refinement is stable for the vast majority of atoms when working at atomic resolution.  ...  To get these hints in a routine way we have implemented two procedures that analyze amplitudes of atomic shifts resulted from several cycles of unrestrained refinement as computer programs [2].  ...  Unrestrained reciprocal space refinement is stable for the vast majority of atoms when working at atomic resolution.  ... 
doi:10.1107/s0108767313098413 fatcat:xda72uczqzgstjdgmipwvsxo74

Prediction of alternative and disordered residues by unrestrained refinement

Oleg Sobolev, Vladimir Y. Lunin
2013 Acta Crystallographica Section A Foundations of Crystallography  
Unrestrained reciprocal space refinement is stable for the vast majority of atoms when working at atomic resolution.  ...  To get these hints in a routine way we have implemented two procedures that analyze amplitudes of atomic shifts resulting from several cycles of unrestrained refinement as computer programs [2].  ...  Unrestrained reciprocal space refinement is stable for the vast majority of atoms when working at atomic resolution.  ... 
doi:10.1107/s0108767313097511 fatcat:szfh5mqm6ba4loieu6edl4evji

Iterative model-based density improvement yields better atomic structures from cryo-EM maps [article]

Arjen J Jakobi, Matthias Wilmanns, Carsten Sachse
2017 bioRxiv   pre-print
We alternate the procedure with consecutive rounds of model refinement and tested it on four cryo-EM structures of TRPV1, β-galactosidase, γ-secretase and RNA polymerase III.  ...  Current cryo-EM model refinement procedures work with the experimental density map that remains constant throughout the process.  ...  520 atomic model, analogous to X-ray crystallography procedures that refine the 521 atomic model against diffraction data.  ... 
doi:10.1101/121913 fatcat:han6geprtvdwxdklconljee24q

Application of statistical potentials to protein structure refinement from low resolutionab initio models

Hui Lu, Jeffrey Skolnick
2003 Biopolymers  
In only seven (four) cases did the refinement procedure increase the RMSD by more than 0.3 (0.5) Å. For the remaining structures, the refinement procedures changed the structures by less than 0.3 Å.  ...  tertiary contact refinement, and statistical pair potential guided molecular dynamics.  ...  [22] [23] [24] In this work, we take the next logical step and develop structure refinement procedures that are guided by these pairwise atomic statistical potentials.  ... 
doi:10.1002/bip.10537 pmid:14648767 fatcat:skeelatnrrdkdc6qz3wclindgu

Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions

T. C. Terwilliger, D. Eisenberg
1983 Acta Crystallographica Section A Foundations of Crystallography  
Sweet, and L. Weissman for useful discussions and Mr F. C. Tsui for the calculations involving data from the B-phycoerythrin crystals. We acknowledge with gratitude support of USPHS grant GM-16925.  ...  A procedure is presented for three-dimensional refinement of heavy-atom parameters without the use of phase information in the methods of single and multiple isomorphous replacement.  ...  One minor disadvantage of the method described here is that, as heavy-atom parameters for each derivative are refined separately, the procedure may not be used to refine the relative positions of heavy  ... 
doi:10.1107/s0108767383001592 fatcat:6h54goqgh5cjvcdufp7a2wuuda
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