Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions.

BMC Bioinformatics
Vladimir PotapovGideon Schreiber

Abstract

Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 A for all residues and 0.73 A for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter perfo...Continue Reading

References

Feb 1, 1992·Protein Science : a Publication of the Protein Society·L Wesson, D Eisenberg
Jan 16, 1986·Nature·D Eisenberg, A D McLachlan
May 1, 1994·Trends in Biotechnology·M W MacArthurJ M Thornton
Oct 1, 1995·Proteins·A V FinkelsteinA M Gutin
Mar 29, 1996·Journal of Molecular Biology·P D Thomas, K A Dill
Mar 1, 1997·Protein Science : a Publication of the Protein Society·J SkolnickA Godzik
Aug 1, 1997·Protein Science : a Publication of the Protein Society·R L Dunbrack, F E Cohen
May 1, 1999·Proteins·T Lazaridis, M Karplus
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 8, 2000·Current Opinion in Structural Biology·T Lazaridis, M Karplus
Aug 10, 2000·Protein Science : a Publication of the Protein Society·R Samudrala, M Levitt
Aug 2, 2001·Journal of Molecular Biology·Z Xiang, B Honig
Oct 6, 2001·Science·D Baker, A Sali
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Nov 25, 2003·Science·Brian KuhlmanDavid Baker
Mar 27, 2004·Protein Science : a Publication of the Protein Society·Nicolae-Viorel BucheteDevarajan Thirumalai
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Apr 20, 2004·Current Opinion in Structural Biology·N-V BucheteD Thirumalai
Jul 12, 2005·Journal of Molecular Biology·Eran EyalVladimir Sobolev
Sep 28, 2005·Proteins·Michael TressAlfonso Valencia
Jul 18, 2006·Current Opinion in Structural Biology·Alan M Poole, Rama Ranganathan
Nov 1, 2006·Protein Science : a Publication of the Protein Society·Min-Yi Shen, Andrej Sali
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Christopher M Summa, Michael Levitt
Jan 8, 2008·Journal of Molecular Biology·Mingyang LuJianpeng Ma
Jun 17, 2008·Protein Science : a Publication of the Protein Society·Mingyang LuJianpeng Ma
Jun 30, 2009·Protein Engineering, Design & Selection : PEDS·Vladimir PotapovGideon Schreiber
Jul 16, 2009·Proteins·Georgii G KrivovRoland L Dunbrack
Aug 15, 2009·PLoS Computational Biology·Mati CohenGideon Schreiber

❮ Previous
Next ❯

Citations

May 27, 2011·BMC Bioinformatics·Liqing TianTaijiao Jiang
Aug 4, 2011·Drug Discovery Today·Subha Kalyaanamoorthy, Yi-Ping Phoebe Chen
Apr 8, 2014·Journal of Chemical Information and Modeling·Matteo TibertiElena Papaleo
Mar 24, 2016·PLoS Computational Biology·Prakash Chandra RathiHolger Gohlke
Jun 9, 2019·International Journal of Molecular Sciences·Maria BatoolSangdun Choi
May 25, 2021·Frontiers in Molecular Biosciences·Sundeep Chaitanya VedithiTom L Blundell
Dec 4, 2012·Journal of Chemical Information and Modeling·Woong-Hee Shin, Chaok Seok
Jan 7, 2020·Journal of Chemical Information and Modeling·Christina NutschelHolger Gohlke

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

PSP
MATLAB
OPUS
MCSA
MC
SCAP
PROBE
PISCES
SCCOMP
CHARMM19

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.