Refinement of macromolecular structures by the maximum-likelihood method

Acta Crystallographica. Section D, Biological Crystallography
G N MurshudovE J Dodson

Abstract

This paper reviews the mathematical basis of maximum likelihood. The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties. The assumption that different parts of a structure might have different errors is considered. A method for estimating sigma(A) using 'free' reflections is described and its effects analysed. The derived equations have been implemented in the program REFMAC. This has been tested on several proteins at different stages of refinement (bacterial alpha-amylase, cytochrome c', cross-linked insulin and oligopeptide binding protein). The results derived using the maximum-likelihood residual are consistently better than those obtained from least-squares refinement.

Citations

Jul 31, 1998·Protein Science : a Publication of the Protein Society·B SchmidG E Schulz
Oct 29, 1998·Protein Science : a Publication of the Protein Society·Y XueS Young
Oct 29, 1998·Protein Science : a Publication of the Protein Society·K JohanssonH Eklund
Feb 7, 2012·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Songying OuyangMifang Liang
Aug 13, 2011·Archives of Microbiology·Sofia MacieiraAlbrecht Messerschmidt
Nov 13, 2010·European Biophysics Journal : EBJ·Janne Kalikka, Jaakko Akola
Apr 28, 2012·Applied Microbiology and Biotechnology·Mor GoldfederAyelet Fishman
Jul 24, 2012·Applied Microbiology and Biotechnology·Stephen G BellLuet-Lok Wong
Sep 19, 2012·Applied Microbiology and Biotechnology·Jingbo MaHongwei Yu
Mar 7, 2013·Applied Microbiology and Biotechnology·Hajer Ben HlimaNushin Aghajari
Apr 2, 2005·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Anne VolbedaJuan C Fontecilla-Camps
Jun 1, 2005·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Núria VallsJuan A Subirana
Jun 9, 2005·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Andreas KarlssonS Ramaswamy
Nov 29, 2008·Extremophiles : Life Under Extreme Conditions·Carrie A RyeJennifer A Littlechild
Apr 17, 2010·Molecules and Cells·Hyunjin MoonJungwoo Choe
Mar 30, 2011·Journal of Inherited Metabolic Disease·Sarah PicaudUdo Oppermann
Feb 20, 2013·Journal of Inherited Metabolic Disease·Naeem ShafqatWyatt W Yue
Jun 13, 2009·Journal of Computer-aided Molecular Design·Melissa R LandonDagmar Ringe
Jul 7, 2011·Journal of Computer-aided Molecular Design·Scott J PollackRoland W Bürli
Oct 20, 2009·Journal of Biomolecular NMR·Carolina CanoHans Robert Kalbitzer
Sep 1, 2006·Journal of Bioenergetics and Biomembranes·Marie-France GiraudAlain Dautant
Mar 12, 2011·The Protein Journal·Zhigang LiuLadislau C Kovari
Mar 16, 2012·The Protein Journal·Xiangwei FeiChaoneng Ji
Jun 21, 2005·Journal of Structural and Functional Genomics·W Bryan ArendallBi-Cheng Wang
Feb 11, 2005·Journal of Structural and Functional Genomics·Ruslan SanishviliDinesh Christendat
Nov 12, 2005·Journal of Structural and Functional Genomics·Qian Steven XuSung-Hou Kim
Mar 8, 2007·Journal of Structural and Functional Genomics·Takuya B HiyamaBi-Cheng Wang
Oct 31, 2007·Journal of Structural and Functional Genomics·Tatiana PetrovaAndrzej Joachimiak
Nov 7, 2007·Journal of Structural and Functional Genomics·Ronnie O FrederickBrian G Fox

❮ Previous
Next ❯

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Landau-Kleffner Syndrome

Landau Kleffner syndrome (LKS), also called infantile acquired aphasia, acquired epileptic aphasia, or aphasia with convulsive disorder, is a rare childhood neurological syndrome characterized by the sudden or gradual development of aphasia (the inability to understand or express language) and an abnormal electroencephalogram. Discover the latest research on LKS here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Related Papers

Acta Crystallographica. Section D, Biological Crystallography
Paul Emsley, Kevin D Cowtan
Acta Crystallographica. Section D, Biological Crystallography
Collaborative Computational Project, Number 4
Journal of Applied Crystallography
Airlie McCoyRandy J Read
Acta Crystallographica. Section D, Biological Crystallography
Victor S Lamzin, K S Wilson
© 2021 Meta ULC. All rights reserved