Template based protein structure modeling by global optimization in CASP11

Proteins
Keehyoung JooJooyoung Lee

Abstract

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorpor...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Jun 5, 1992·Science·G H GonnetS A Benner
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Feb 14, 2003·Bioinformatics·Nickolai Alexandrov, Ilya Shindyalov
Nov 9, 2004·Bioinformatics·Johannes Söding
Apr 26, 2005·Nucleic Acids Research·Yang Zhang, Jeffrey Skolnick
Oct 19, 2006·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jinbo Xu
Mar 16, 2007·Physical Review Letters·K I LeeJ-H Park
Sep 27, 2007·Proteins·Keehyoung JooJooyoung Lee
Aug 12, 2008·Biophysical Journal·Keehyoung JooJooyoung Lee
Jul 16, 2009·Proteins·Georgii G KrivovRoland L Dunbrack
Jan 1, 2009·Research in Computational Molecular Biology : ... Annual International Conference, RECOMB ... : Proceedings·Jian Peng, Jinbo Xu
Sep 26, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Juyong LeeJooyoung Lee
Jul 16, 2013·Scientific Reports·Juyong LeeJooyoung Lee
Dec 11, 2013·Proteins·Yuanpeng J HuangGaetano T Montelione
Mar 29, 2014·Proteins·Hyun Joo, Jerry Tsai
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

❮ Previous
Next ❯

Citations

Nov 4, 2016·The Journal of Physical Chemistry. B·Jeffrey Skolnick, Hongyi Zhou
Oct 30, 2016·Journal of Chemical Information and Modeling·Magdalena A MozolewskaCezary Czaplewski
Feb 2, 2018·Bioinformatics·Mindaugas Margelevicius
Oct 5, 2017·Proteins·Tianyun LiuRuss B Altman
Jul 18, 2017·Nature Microbiology·Mi-Jeong KwakByung-Ha Oh
Aug 9, 2019·Journal of Clinical Medicine·Yonggoo KimMyungshin Kim
Aug 5, 2017·Acta Crystallographica. Section D, Structural Biology·Su Datt LamChristine Orengo
Dec 18, 2019·PLoS Computational Biology·Giacomo JansonAlessandro Paiardini
Nov 22, 2017·Proteins·Seung Hwan HongJooyoung Lee
Apr 19, 2017·Bioinformatics·Balachandran Manavalan, Jooyoung Lee
Jan 18, 2018·Proteins·Keehyoung JooJooyoung Lee
Aug 12, 2017·Journal of Chemical Theory and Computation·Qianyi ChengJooyoung Lee
Jan 31, 2020·Journal of Chemical Information and Modeling·Agnieszka S KarczyńskaCezary Czaplewski
Jun 14, 2019·The Journal of Physical Chemistry. B·Adam K SieradzanMariusz Makowski

❮ Previous
Next ❯

Related Concepts

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections 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.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

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.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation 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.