NDLI: A NMR-spectra-based scoring function for protein docking

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A NMR-spectra-based scoring function for protein docking

Content Provider	ACM Digital Library
Author	Burchardt, A. Hildebrandt, A. Bayer, P. Lenhof, H.-P Kohlbacher, O. Moll, A.
Abstract	A well studied problem in the area of Computational Molecular Biology is the so-called Protein-Protein Docking problem (PPD) that can be formulated as follows: Given two proteins A and B that form a protein complex, compute the 3D-structure of the protein complex AB. Protein docking algorithms can be used to study the driving forces and reaction mechanisms of docking processes. They are also able to speed up the lenghty process of experimental structure elucidation of protein complexes by proposing potential structures. In this paper, we are discussing a variant of the PPD-problem where the input consists of the tertiary structures of A and B plus an unassigned $^{1}H-NMR$ spectrum of the complex AB. We present a new scoring function for evaluating and ranking potential complex structures produced by a docking algorithm. The scoring function computes a “theoretical” $^{1}H-NMR$ spectrum for each tentative complex structure and subtracts the calculated spectrum from the experimental spectrum. The absolute areas of the difference spectra are then used to rank the potential complex structures. In contrast to formerly published approaches (e.g. Morelli et. al. [38]) we do not use distance constraints (intermolecular NOE constraints). We have tested the approach with the bound conformations of four protein complexes whose three-dimensional structures are stored in the PDB data bank [5] and whose $^{1}H-NMR$ shift assignments are available from the BMRB database (BioMagResBank [47]).In all examples, the new scoring function produced very good rankings of the structures. The best result was obtained for an example, where all standard scoring functions failed completely. Here, our new scoring function achieved an almost perfect separation between good approximations of the true complex structure and false positives.Unfortunately, the number of complexes with known structure and available spectra is very small. Nevertheless, these experiments indicate that scoring functions based on comparisons of one- or multi-dimensional NMR spectra might be a good instrument to improve the reliability and accuracy of docking predictions and perhaps also of protein structure predictions (threading).
Starting Page	184
Ending Page	192
Page Count	9
File Format	PDF
ISBN	1581133537
DOI	10.1145/369133.369194
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2001-04-22
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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