Scoring protein interaction decoys using exposed residues (SPIDER): a novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues.

Proteins
Raed KhashanAlexander Tropsha

Abstract

Accurate prediction of the structure of protein-protein complexes in computational docking experiments remains a formidable challenge. It has been recognized that identifying native or native-like poses among multiple decoys is the major bottleneck of the current scoring functions used in docking. We have developed a novel multibody pose-scoring function that has no theoretical limit on the number of residues contributing to the individual interaction terms. We use a coarse-grain representation of a protein-protein complex where each residue is represented by its side chain centroid. We apply a computational geometry approach called Almost-Delaunay tessellation that transforms protein-protein complexes into a residue contact network, or an undirectional graph where vertex-residues are nodes connected by edges. This treatment forms a family of interfacial graphs representing a dataset of protein-protein complexes. We then employ frequent subgraph mining approach to identify common interfacial residue patterns that appear in at least a subset of native protein-protein interfaces. The geometrical parameters and frequency of occurrence of each "native" pattern in the training set are used to develop the new SPIDER scoring function....Continue Reading

References

Dec 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·A Godzik, J Skolnick
Sep 5, 1992·Journal of Molecular Biology·A GodzikJ Skolnick
Mar 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E Katchalski-KatzirI A Vakser
Jan 1, 1996·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·R K SinghI I Vaisman
Feb 1, 1997·Protein Science : a Publication of the Protein Society·J A Rank, D Baker
Sep 23, 1997·Journal of Molecular Biology·H A GabbM J Sternberg
Feb 2, 1999·Journal of Molecular Biology·L Lo ConteJ Janin
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Jul 13, 2000·Protein Science : a Publication of the Protein Society·C CzaplewskiH A Scheraga
Jun 5, 2003·Proteins·Joël JaninUNKNOWN Critical Assessment of PRedicted Interactions
Apr 2, 2005·Protein Science : a Publication of the Protein Society·Chu WangDavid Baker
Nov 5, 2005·Alternatives to Laboratory Animals : ATLA·Joanna JaworskaTom Aldenberg
Aug 25, 2006·Bioinformatics·Dominique DouguetIlya A Vakser
Jul 12, 2007·Proteins·Julian MintserisZhiping Weng
Oct 9, 2007·Proteins·Marc F LensinkShoshana J Wodak
Apr 3, 2008·PloS One·Hongbo ZhuFrancisco S Domingues
Jul 22, 2009·Bioinformatics·José Ignacio GarzonPablo Chacon
Jun 24, 2010·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Deepak BandyopadhyayAlexander Tropsha
Sep 2, 2010·Proteins·Howook HwangZhiping Weng
Jan 11, 2011·Journal of Chemical Information and Modeling·Carles PonsJuan Fernandez-Recio
Jun 16, 2011·Journal of Structural and Functional Genomics·Michael T ZimmermannAndrzej Kloczkowski
Oct 18, 2011·Journal of Molecular Biology·Sarel J FleishmanDavid Baker
Jul 12, 2010·Molecular Informatics·Alexander Tropsha

❮ Previous
Next ❯

Citations

Oct 2, 2013·BMC Bioinformatics·Iain H MoalJuan Fernández-Recio
Nov 30, 2012·Briefings in Bioinformatics·Weiqiang Zhou, Hong Yan
Jun 8, 2014·BMC Bioinformatics·Reyhaneh Esmaielbeiki, Jean-Christophe Nebel
Jul 4, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Romina OlivaLuigi Cavallo
Oct 1, 2013·Molecular Informatics·Denis Fourches, Alexander Tropsha
Mar 5, 2014·The FEBS Journal·Anne T Tuukkanen, Dmitri I Svergun
Mar 5, 2014·The FEBS Journal·João P G L M Rodrigues, Alexandre M J J Bonvin
Mar 6, 2015·Proteins·James D Alsop, Julie C Mitchell
Sep 3, 2014·Proteins·Marc F Lensink, Shoshana J Wodak
Jun 21, 2015·Journal of Theoretical Biology·Sumaiya IqbalMd Tamjidul Hoque
Jul 23, 2013·Current Opinion in Structural Biology·Iain H MoalJuan Fernández-Recio
Jun 17, 2016·Bioinformatics·Sankar Basu, Björn Wallner
Jan 24, 2009·Current Opinion in Structural Biology·Olgun Guvench, Alexander D MacKerell
Dec 29, 2017·Journal of Cheminformatics·Ting FengTingjun Hou
Feb 6, 2017·Journal of Computational Chemistry·Baofeng ZhangEmilio Gallicchio
Dec 3, 2016·The Journal of Biological Chemistry·Allison B GoldbergBenjamin E Turk
Nov 17, 2020·Frontiers in Molecular Biosciences·Guillaume LaunayJuliette Martin

❮ 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.