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Contact
Publications
Other research publications
Book chapter
Conference Talks
Software and libraries
Web applications
Software screenshots

Contact information

Maxim Shapovalov, PhD
Former Senior Programmer Analyst

Former member of Dr. Roland Dunbrack Lab
Basic Science Division, Biomolecular Structure and Function

Mailing address:

Maxim Shapovalov
c/o Dr. Roland Dunbrack
Fox Chase Cancer Center
333 Cottman Avenue
Philadelphia, PA 19111
USA

E-mail: ( please replace " _dot~ " with " . " and " *at# " with " @ " respectively )

Phone: hidden for security purposes

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Software, libraries, websites and publications

Publications

Software and library

[1] Adolf-Bryfogle, J., Labonte J., Kraft J., Shapovalov M., et al. Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. bioRxiv 2021.09.27.462000

[2] Shapovalov, M, Dunbrack, RL, Jr., and Vucetic, S. Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction. PLOS ONE, 2020. 15(5): e0232528.

[3] Shapovalov, M. Machine Learning Algorithms for Characterization and Prediction of Protein Structural Properties. Doctoral Dissertation, Temple University, 2019. Publication #: 20.500.12613/2356.

[4] Shapovalov, M, Vucetic, S, and Dunbrack, RL, Jr. A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PLoS Comput Biol, 2019. 15(3): e1006844.

[5] Alford, R, Leaver-Fay, A, Jeliazkov, J, O'Meara, M, DiMaio, F, Park, H, Shapovalov, M, et al. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. Journal of chemical theory and computation, 2017. 13(6): p. 3031-3048.

[6] Shapovalov, MV, Wang, Q, Xu, Q, Andrake, M, and Dunbrack Jr, RL. Bioassemblymodeler (BAM): User-friendly homology modeling of protein homo-and heterooligomers. PLOS ONE, 2014. 9(6): e98309.

[7] Shapovalov, MV and Dunbrack, RL, Jr. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure, 2011. 19(6): p. 844-58.

[8] Ting, D, Wang, G, Shapovalov, M, Mitra, R, Jordan, MI, and Dunbrack, RL, Jr. Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol, 2010. 6(4): e1000763.

[9] Krivov, GG, Shapovalov, MV, and Dunbrack, RL, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 2009. 77(4): p. 778-95.

[10] Xu, Q, Canutescu, AA, Wang, G, Shapovalov, M, Obradovic, Z, and Dunbrack, RL, Jr. Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol, 2008. 381(2): p. 487-507.

[11] Shapovalov, MV and Dunbrack, RL, Jr. Statistical and conformational analysis of the electron density of protein side chains. Proteins: Structure, Function and Genetics, 2007. 66(2): p. 279-303.

[12] Shapovalov, MV, Canutescu, AA, and Dunbrack, RL, Jr. BioDownloader: Bioinformatics downloads and updates in a few clicks. Bioinformatics, 2007. 

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Book chapter

[13] Shapovalov, M and Dunbrack Jr, RL. Non-parametric statistical analysis of the Ramachandran map in Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map. 2013, World Scientific. p. 76-94.

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Other research publications

[14] Lehmann, A, Wixted, JH, Shapovalov, MV, Roder, H, Dunbrack, RL, Jr., and Robinson, MK. Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach. MAbs, 2015. 7(6): p. 1058-71.

[15] Berkholz, DS, Driggers, CM, Shapovalov, MV, Dunbrack, RL, Jr., and Karplus, PA. Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proc Natl Acad Sci U S A, 2012. 109(2): p. 449-53.

[16] Beglov, D, Hall, DR, Brenke, R, Shapovalov, MV, Dunbrack, RL, Jr., Kozakov, D, and Vajda, S. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins, 2011.

[17] Shandler, SJ, Shapovalov, MV, Dunbrack, RL, Jr., and DeGrado, WF. Development of a rotamer library for use in beta-peptide foldamer computational design. J Am Chem Soc, 2010. 132(21): p. 7312-20.

[18] Loll, PJ, Derhovanessian, A, Shapovalov, MV, Kaplan, J, Yang, L, and Axelsen, PH. Vancomycin forms ligand-mediated supramolecular complexes. J Mol Biol, 2009. 385(1): p. 200-11.

[19] Berkholz, DS, Shapovalov, MV, Dunbrack, RL, Jr., and Karplus, PA. Conformation dependence of backbone geometry in proteins. Structure, 2009. 17(10): p. 1316-25.

[20] Karplus, PA, Shapovalov, MV, Dunbrack, RL, Jr., and Berkholz, DS. A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallogr D Biol Crystallogr, 2008. 64(Pt 3): p. 335-6.

[21] Antoniou, I, Ivanov, VV, Kryanev, AV, Matokhin, VV, and Shapovalov, MV. On the efficient resources distribution in economics based on entropy. Physica A: Statistical Mechanics and its Applications, 2004. 336(3): p. 549-562.

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Conference talks

1) Shapovalov M, Wang G, Dunbrack RL Jr. New Ramachandran Maps and the Next Generation of the Backbone-Dependent Rotamer Library. University of Washington Rosetta Conference (RosettaCON), Leavenworth, WA, USA, 2008.

2) Shapovalov M, Dunbrack RL Jr. The Next Generation of the Backbone-dependent Rotamer Library. 3DSIG, Conference on Intelligent Systems in Molecular Biology (ISMB), Toronto, Canada, 2008.

3) Shapovalov M, Xu Q, Wang G, Ting D, Jordan MI, Dunbrack RL Jr. Statistical Analysis of Protein Structures: Electron Density, Conformational Analysis, and Protein-protein Interfaces. American Crystallographic Association Meeting (ACA), Knoxville, TN, USA, 2008.

4) Shapovalov MV, Dunbrack RL Jr. Using electron density in structural bioinformatics. Highlights Session, Structural Bioinformatics Meeting at ISMB, Austria, 2007.

5) Xu Q, Canutescu A, Shapovalov M, Wang G, Dunbrack RL Jr. Structural bioinformatics reveals probable biological interfaces in protein crystals. 3DSIG, Conference on Intelligent Systems in Molecular Biology (ISMB), Austria, 2007.

6) Xu Q, Canutescu AA, Shapovalov MV, Dunbrack RL Jr. Identifying biologically relevant interfaces in protein crystals. American Chemical Society, Boston, USA, 2007 Aug 19-23.

7) Shapovalov MV, Dunbrack RL Jr. Using Statistical Analysis of Electron Density to Evaluate Protein Side-Chain Conformations and Rotamer Disorder. Structural Bioinformatics Meeting at ISMB, Scotland, 2004 Jul 21;31.

8) Shapovalov MV. Improving protein structure analysis and prediction by using electron denisty maps. Moscow Engineering Physics Institute Scientific Session, Russia, 2004;T-7:118-9.

9) Kryanev AV, Matokhin VV, Shapovalov MV. Assessment of resources disribution efficiency using two-parameter control function family. Moscow Engineering Physics Institute Scientific Session, Russia, 2002;T-7:101-2.

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Software and libraries:

SecNet

Deep convolutional neural network with 2% higher prediction accuracy for a 50-year-old problem of protein secondary structure prediction; in the last 20 years, 140 teams improved accuracy only by 3%; our improvement translates to 13 years of research with only 2 years of development; github.com/sh-maxim/ss

βTurnTool18 and βTurnLib18

Assignment turn tool and library compiled with hierarchical DBSCAN and kMedoids clustering of 13 thousand of 3D protein fragments; 11 new types are discovered and 1 is eliminated; 2,700 downloads; github.com/sh-maxim/BetaTurn18

BAM (BioAssemblyModeler)

GUI application for 3D modeling of protein complexes; 2,200 users and 500 users of the first and second versions; dunbrack.fccc.edu/BAM

SCWRL4

Cross-platform (Unix/Windows/Mac) program for atomic modeling of protein side chains; the most popular in the field; many commercial licenses; 9,000 users; dunbrack.fccc.edu/scwrl4

Rotamer Library

Statistically derived representation of protein side-chain atomic conformations, compiled from 4,000 protein structures using adaptive kernel density estimation and kernel regression of response variables; 900 users; dunbrack.fccc.edu/bbdep2010

BioDownloader

GUI application for downloading, updating and routine processing of biological files from FTP and HTTP servers; 650 users; dunbrack.fccc.edu/BioDownloader

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Web applications (Development and/or Administration)

dunbrack2.fccc.edu/ProtCiD

Microsoft web server frontend for a Firebird database of protein interfaces. It supports different modes of querying and GUI browsing. For custom queries it allows submitting Linux jobs to a designated Linux server for additional computing and then retrieves results back.

dunbrack2.fccc.edu/PyIgClassify

Frontend of an SQLite database of antibody 3D conformations compiled with clustering.

dunbrack.fccc.edu/kincore

Python Flask web application of kinase conformation database.

dunbrack.fccc.edu

RHEL8, Apache web server for our research group content and product licensing.

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Software screenshots

BAM - GUI application for 3D homology modeling of protein complexes:

BAM

Multi-conformational analysis of protein electron density:

ElectronDensity

BioDownloader - GUI application for downloading, updating and routine processing of biological files from FTP and HTTP servers:

BioDownloader

BbDep2010 - Statistically derived representation of protein side-chain atomic conformations, compiled from 4,000 protein structures using adaptive kernel density estimation and kernel regression of response variables:

RotamerLibraryArt

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webdesign: Maxim V. Shapovalov and Adrian A. Canutescu

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