Publications

Selected Publications - ICM Methods and Applications

2008

Cavasotto CN, Orry AJ, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML, Monsma FJ Jr.
Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening. J Med Chem. 2008 Jan 17; [Epub ahead of print]

2007

Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E.
3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18619-24.

Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE.
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput Aided Mol Des. 2007 Oct-Nov;21(10-11):549-58.

Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ, Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA.
Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates. J Med Chem. 2007 Nov 1;50(22):5357-63.

Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA.
De novo discovery of serotonin N-acetyltransferase inhibitors. J Med Chem. 2007 Nov 1;50(22):5330-8.

Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P.
Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition. J Biol Chem. 2007 Dec 14;282(50):36505-13.

Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ.
Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues. J Biol Chem. 2007 Nov 9;282(45):32834-43.

Bisson WH, Cheltsov AV, Bruey-Sedano N, Lin B, Chen J, Goldberger N, May LT, Christopoulos A, Dalton JT, Sexton PM, Zhang XK, Abagyan R.
Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):11927-32.

Outeiro TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, Amore AM, Volk CB, Maxwell MM, Rochet JC, McLean PJ, Young AB, Abagyan R, Feany MB, Hyman BT, Kazantsev AG.
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease. Science. 2007 Jul 27;317(5837):516-9.

Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini JC, Abagyan R.
Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening. Biochem Biophys Res Commun. 2007 Jul 6;358(3):686-91.

Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ.
Molecular approximations between residues 21 and 23 of secretin and its receptor: development of a model for peptide docking with the amino terminus of the secretin receptor. Mol Pharmacol. 2007 Aug;72(2):280-90.

Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R.
PIER: Protein interface recognition for structural proteomics. Proteins. Feb13 Epub 2007 [NCBI_Abstract]

2006

Budagyan L, Abagyan R.
Weighted quality estimates in machine learning.
Bioinformatics. 2006 Nov 1;22(21):2597-603. [NCBI_Abstract]

Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG.
Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells.
Chem Biol. 2006 Jul;13(7):765-70. [NCBI_Abstract]

Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S.
Defining the CD59-C9 binding interaction.
J Biol Chem. 2006 Sep 15;281(37):27398-404. [NCBI_Abstract]

Orry AJ, Abagyan RA, Cavasotto CN.
Structure-based development of target-specific compound libraries.
Drug Discov Today. 2006 Mar;11(5-6):261-6. [NCBI_Abstract]

Bordner AJ, Abagyan R.
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.
Proteins. 2006 May 15;63(3):512-26. [NCBI_Abstract]

Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD.
Disseminating structural genomics data to the public: from a data dump to an animated story.
Trends Biochem Sci. 2006 Jan 4 [NCBI_Abstract]

Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ.
In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells.
Bioorg Med Chem Lett. 2006 Jan 11 [NCBI_Abstract]

2005

Cardozo T, Abagyan R.
Druggability of SCF Ubiquitin Ligase-Protein Interfaces.
Methods Enzymol. 2005;399:634-53. [NCBI_Abstract]

Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S.
Insights into the human CD59 complement binding interface toward engineering new therapeutics.
J Biol Chem. 2005 Oct 7;280(40):34073-9 [NCBI_Abstract]

Cavasotto, C.N., Orry, A.J.W., Abagyan R.
The challenge of considering receptor flexibility in ligand docking and virtual screening.
Curr. Comput. Aided Drug Des. 2005. 1, 423-440

Cavasotto CN, Kovacs JA, Abagyan RA.
Representing receptor flexibility in ligand docking through relevant normal modes.
J Am Chem Soc. 2005 Jul 6;127(26):9632-40. [NCBI_Abstract]

Fernandez-Recio J, Abagyan R, Totrov M.
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Proteins. 2005 Aug 1;60(2):308-13. [NCBI_Abstract]

Bordner AJ, Abagyan R.
Statistical analysis and prediction of protein-protein interfaces.
Proteins. 2005 Aug 15;60(3):353-66. [NCBI_Abstract]

An J, Totrov M, Abagyan R.
Pocketome via comprehensive identification and classification of ligand binding envelopes.
Mol Cell Proteomics. 2005 Jun;4(6):752-61.[NCBI_Abstract]

Cavasotto, C.N., Orry, A.J.W., Abagyan R.
Receptor Flexibility in Ligand Docking.
In Handbook of Theoretical and Computational Nanotechnology American Scientific. Publishers. Eds. Michael Rieth, Wolfram Schommers.

Fernandez-Recio, J., Totrov, M., Skorodumov, C., Abagyan, R.
Optimal Docking Area: A New Method for Predicting Protein-Protein Interaction Sites.
Proteins 57:400-13. [NCBI_Abstract]

2004

An, J., Totrov, M., Abagyan, R.
Comprehensive identification of "druggable" protein ligand binding sites.
Genome Inform Ser Workshop Genome Inform., 15(2):31-41. [NCBI_Abstract]

Bordner, A., and Abagyan, R.

Large-Scale Prediction of Protein Geometry and Stability Changes for Arbitrary Single-Point Mutations.
Proteins 57:400-13. [NCBI_Abstract]

Marsden, B., and Abagyan, R.
SAD - A normalized structural alignment database: improving sequence-structure alignments.
Bioinformatics, 20:2333-44. [NCBI_Abstract]

Cavasotto, C.N., Liu, G., James, S., Hobbs, P., Peterson, V., Bhattacharya, A., Kolluri, S., Zhang, X., Leid, M., Abagyan, R., Liddington, R., and Dawson, M.
Determinants of Retinoid X Receptor Transcriptional Antagonism
J. Med. Chem., 47:4360-72. [NCBI_Abstract]

Kovacs, J. Chacon, P., and Abagyan, R.
Predictions of Proteins Flexibility: First Order Measures.
Proteins, 56:661-8. [NCBI_Abstract]

Hill, T., Odell, L., Quan, A., Abagyan, R., Ferguson, G., Robinson, P., McCluskey, A.
Long Chain Amines and Long Chain Ammonium Salts as Novel Inhibitors of Dynamin GTPase Activity
Bioorganic Med Chem Letters Jun 21; 14(12): 3275-8 [NCBI_Abstract]

Fernandez-Recio, J., Totrov, M.M., and Abagyan, R.
Identification of Protein-Protein Interaction Sites From Docking Energy Landscapes

J. Mol. Biol. Jan 16; 335(3): 843-65. [NCBI_Abstract]

Cavasotto, C.N. and Abagyan, R.A.
Protein Flexibility in Ligand Docking and Virtual Screening To Protein Kinases
J. Mol. Biol. Mar 12; 337(1): 209-25 [NCBI_Abstract]

2003

Bordner, A.J., Cavasotto, C.N., and Abagyan, R.A.
Direct Derivation of Van der Waals Force Field Parameters From Quantum Mechanical Interaction Energies
J. Phys. Chem. B. 107: 9601-9609

Katritch, V., Totrov, M.M. and Abagyan, R.A.

Cavasotto, C., Orry, A.J.W., and Abagyan, R.A.
Structure-Based Identification of Binding Sites, Native Ligands and Potential Inhibitors for G-Protein Coupled Receptors
Proteins: Structure, Function, and Genetics 51(3), 423-433 [NCBI_Abstract]

Schapira, M.,Raaka, B., Das, S., Fan, L., Totrov, M., Zhou, Z., Wilson, S., Abagyan, R. and Samuels, H.
Discovery of Diverse Thyroid Hormone Receptor Antagonists by High-Throughput Docking

PNAS 100(12), 7354-7359 [NCBI_Abstract]

Fernandez-Recio, J., Totrov, M., and Abagyan, R.
ICM-DISCO Docking by Global Energy Optimization with Fully Flexible Side-Chains
Proteins 52:113-117 [NCBI_Abstract]

Schapira, M., Abagyan, R.A. and Totrov, M.M.
Nuclear Hormone Receptor Targeted Virtual Screening
J. Med. Chem. ASAP Article. 10.1021 [NCBI_Abstract]

Bursulaya, B., Totrov, M.M., Abagyan, R.A., and Brooks, C.
Comparative Study of Several Algorithms For Flexible Ligand Docking
J. Comp. Aided Mol. Design 17: 755-63 [NCBI_Abstract]

Marsden, B., and Abagyan, R.
Identifying Errors in Three-Dimensional Protein Models
Protein Structure: Determination, Analysis, and Applications for Drug Discovery, Daniel Chasman, Ed. Marcel Dekker, Inc. (Basel) 277-313 -

2002

Fernandez-Recio, J., Totrov, M.M., and Abagyan, R.A.
Soft Protein-Protein Docking in Internal Coordinates
Protein Science 11:280-91 [NCBI_Abstract]

Brive, L, and Abagyan, R.A.
Computational Structural Proteomics
Ernst Schering Res Found Workshop (38): 149-66 (Berlin) [NCBI_Abstract]

Schapira, M., Abagyan, R.A. and Totrov, M.M.
Structural Model of Nicotinic Acetylcholine Receptor Isotypes Bound to Acetylcholine and Nicotine.
BMC Structural Biology Journal 2(1):1. [NCBI_Abstract]

Bordner, A.J.,Cavasotto,C.N. and Abagyan,R.A.
Accurate Transferable Model for Water, N-Octanol, and N-Hexadecane Solvation Free Energies
J. Phys. Chem. B. 106:11009

2001

Abagyan, R.A. and Totrov, M.M.

High-Throughput Docking for Lead Generation
Current Opinion in Chemical Biology Aug;5(4):375-82 [NCBI_Abstract]

Norledge, B.V., Lambeir, A.M., Abagyan, R.A., Rottmann, A., Fernandez, A.M., Filimonov, V., Peter, M.G., and Wierenga, R.K.
Modeling, Mutagenesis, and Structural Studies on the Fully Conserved Phosphateloop (Loop 8) of Triosephosphate Isomerase: Toward a New Substrate Specificity
Proteins Feb 15;42(3), 383-9 [NCBI_Abstract]

Schapira, M., Raaka, B.M., Samuels, H.H., and Abagyan, R.A.
In Silico Discovery of Novel Retinoic Acid Receptor Agonist Structures
BMC Structural Biology Journal 2001;1(1):1 [NCBI_Abstract]

Totrov, M.M., and Abagyan, R.A.
Protein-Ligand Docking as an Energy Optimization Problem

Drug-Receptor Thermodynamics: Introduction and Applications. Editor: R.B. Raffa John Wiley & Sons, RV, 603-624

Totrov, M.M., and Abagyan, R.A.
Rapid Boundary Element Solvation Electrostatics Calculations in Folding Simulations: Successful Folding of a 23-Residue Peptide
Biopolymers 2001;60(2):124-33 [NCBI_Abstract]

2000

Cardozo, T., Batalov, S., and Abagyan, R.A.
Estimating Local Backbone Structural Deviation in Homology Models
Computers & Chemistry Jan 24(1), 13-31 [NCBI_Abstract]

Filikov, A.V., Mohan, V., Vickers, T.A., Griffey, R.H., Cook, P.D., Abagyan, R.A., and James, T.L.
Identification of Ligands For HIV-1 TAR RNA Via Structure Based Virtual Screening
JCAMD Aug 14(6), 593-610 [NCBI_Abstract]

Gantt, S., Persson, C., Rose, K., Birkett, A.J., Abagyan, R.A. and Nussenzweig, V.
Antibodies Against Trap Do Not inhibit Plasmodium Sporozoite infectivity in Vivo

Infection and Immunity Jun; 68(6), 3667-3673 [NCBI_Abstract]

Jin, E., Katritch, V., Olson, W.K., Kharatisvili, M., Abagyan, R.A., and Pilch, D.S.
Aminoglycoside Binding in The Major Groove of Duplex RNA: The Thermodynamic and Electrostatic Forces that Govern Recognition
J. Mol. Biol. Apr 21 298 (1), 95-110 [NCBI_Abstract]

Kelly, P.D., Chu, F., Wood, I.G., Ngo-Hazelett, P., Cardozo, T., Huang, H., Kimm, F., Liao, L., Yan, Y.L., Zhou, Y., Johnson, S.L., Abagyan, R.A., Schier, A.F., Postlethwait, J.H. and Talbot, W.S.
Genetic Linkage Mapping of Zebrafish Genes and ESTs
Genome Res Apr. 10 (4), 558-567 [NCBI_Abstract]

Schapira, M., Raaka, B.M., Samuels, H, H. and Abagyan, R.A.
Rational Discovery of Novel Nuclear Hormone Receptor Antagonists

PNAS Feb 1;97 (3), 1008-1013 [NCBI_Abstract]

Tomko, R.P., Totrov, M.M., Abagyan, R.A. and Philipson, L.
Expression of the Adenovirus Receptor and its Interaction with the Fiber Knob
Experimental Cell Research Feb 25;255(1), 47-55 [NCBI_Abstract]

1999

Abagyan, R.A. and Totrov, M.M.
Ab Initio Folding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure
Journal of Computational Physics 151, 402-421

Gates, M., Kim, L., Egan, E., Cardozo, T., Sirotkin, H., Dougan, S., Lashkari, D., Davis, R., Abagyan, R.A., Schier, A,. and Talbot, W.

An Integrated Genetic Linkage Map of the Zebrafish Genome
Genome Research 9, 334-47 [NCBI_Abstract]

Li, D., Desai-Yajnik, V., Lo, E., Schapira, M., Abagyan, R.A., and Samulels, H.H.
NRIF3 Is a Novel Co-Activator Mediating Functional Specificity of Nuclear Hormone Receptors
Molecular and Cellular Biology Oct, 19 (10), 7191-7202 [NCBI_Abstract]

Schapira, M., Totrov, M.M., and Abagyan, R.A.
Prediction of the Binding Energy for Small Molecules, Peptides and Proteins
J. of Molecular Recognition 12, 177-190 [NCBI_Abstract]

Stigler, R.-D., Hoffmann, B, Abagyan, R.A. and Schneider-Mergener, J.
Soft Docking an L and a D Peptide to an Anticholera Toxin Antibody Using Internal Coordinate Mechanics

Structure 7, 663-670 [NCBI_Abstract]

Totrov, M.M., and Abagyan R.A.
Derivation of Sensitive Discrimination Potential for Virtual Ligand Screening
Proceedings of the Third Annual Intl. Conf. on Comp. Mol. Bio. 312-320

Zhang, H-F., Yu, J., Chen, S., Morgan, B.P., Abagyan, R.A. and Tomlinson, S.
Identification of the Individual Residues that Determine Human Cd59 Species Selective Activity
J.Biol.Chem. 274, 10969-10974 [NCBI_Abstract]

Zhou, Y., and Abagyan, R.A.
Efficient Stochastic Global Optimization for Protein Structure Prediction

Rigidity Theory and Application (M.F. Thorpe & P.M. Duxbury eds.) 345-356

1998

Cardozo, T.J. and Abagyan, R.A.
Molecular Modeling of the Domain Shared Between CED-4 and its Mammalian Homologue APAF-1: A Structural Relationship to the G-Proteins
J. of Mol. Model. 4, 83-93

Patel, I.R., Attur, M.G., Patel, R.N., Stuchin, S.A., Abagyan, R.A., Abramson, S.B., and Amin, A.R.
TNF-A Convertase Enzyme From Human Arthritis-Affected Cartilage: Isolation of CDNA by Differential Display, Expression of the Active Enzyme, and Regulation of Tnf-A
J. of Immunology 160, 4570-4579 [NCBI_Abstract]

Maiorov, V. and Abagyan, R.A.
Energy Strain in Three-Dimensional Protein Structures

Folding & Design 3, 259-269 [NCBI_Abstract]

Isakoff, S.J., Cardozo, T., Andreev, J., Li, Z., Ferguson, K.M., Abagyan, R.A., Lemmon, M.A., Aronheim, A and Skolnik, E.Y.
Identification and Analysis of Ph Domain-Containing Targets of Phosphatidylinositol 3-Kinase Using a Novel In Vivo Assay in Yeast
Embo J. 17 (18), 5374-87 [NCBI_Abstract]

Zhou, Y. and Abagyan, R.A.
How and Why Phosphotyrosine-Containing Peptides Bind to the SH2 and PTB Domains
Folding and Design 3, 513-522 [NCBI_Abstract]

Srivastava, S., Osten, P., Vilim, F.S.,Khatri, L., Inman, G., States, B., Daly, C., DeSouza, S., Abagyan, R.A., Valtschanoff, J.G., Weinberg, R.J. and Ziff, E.B.
Novel Anchorage of Glur2/3 to the Postsynaptic Density by the AMPA Receptor-Binding Protein ABP

Neuron 21, 581-591 [NCBI_Abstract]

1997

Thanki, N., Zeelen, J.Ph., Mathieu, M., Jaenicke, R., Abagyan, R.A., Wierenga R.K., and Schliebs, W.
Protein Engineering With Monomeric Triosephosphate Isomerase (Monotim): The Modelling and Structure Verification of A Seven Residue Loop
Protein Eng. 10, 159-167 [NCBI_Abstract]

Maiorov, V.N., and Abagyan, R.A.
A New Method for Modeling Large-Scale Rearrangements of Protein Domains
Proteins 27, 410-424 [NCBI_Abstract]

Yu, J., Abagyan, R., Dong, S., Gilbert, A., Nusenzweig, V., and Tomlinson, S.
Mapping of the Active Site of CD59

J. Expt. Medicine 185, 745-754 [NCBI_Abstract]

Abagyan, R.A., and Batalov, S.V.
Do Aligned Sequences Share The Same Fold?
J. Mol. Biol. 273, 355-368 [NCBI_Abstract]

Abagyan, R., and Totrov, M.
Contact Area Difference (CAD): A Robust Measure to Evaluate Accuracy of Protein Models
J. Mol. Biol. 268, 678-285 [NCBI_Abstract]

Yu, J., Dong, S., Rushmere, N.K., Morgan, B.P., Abagyan, R.A., and Tomlinson, S.
Mapping The Regions of The Complement Inhibitor CD59 Responsible for its Species Selective Activity

Biochemistry 36, 9423-9428 [NCBI_Abstract]

Koonin, E.V. and Abagyan, R.A.
TSG101 May Be the Prototype of A Class of Dominant Negative Ubiquitin Regulators
Nature Genetics 16, 330-331 [NCBI_Abstract]

Abagyan, R.A., Batalov, S., Cardozo, T., Totrov, M., and Zhou, Y.
Homology Modeling With ICM: Deformation Zone Mapping and Improvements of Models Via Conformational Search
Proteins Supplement 1, 29-37 [NCBI_Abstract]

Totrov, M.M., and Abagyan, R.A.
Flexible Protein-Ligand Docking by Global Energy Optimization in Internal Coordinates

Proteins Supplement 1, 215-220 [NCBI_Abstract]

Abagyan, R.A.
Protein Structure Prediction by Global Energy Optimization
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (van Gunsteren, W.F., et al., eds.). 3, 363-394

Rashin, A.A., Rashin, B.H., Rashin A., and Abagyan, R.
Evaluating the Energetics of Empty Cavities and Internal Mutations in Proteins
Protein Science 6, 2143-2158 [NCBI_Abstract]

Mathieu, M., Modis, Y., Zeelen, J. Ph., Engel, C.K., Abagyan, R.A., Ahlberg, A., Rasmussen, B., Lamzin, V.S., Kunau W.H., and Wierenga, R.K.
The 1.8 Crystal Structure of the Dimeric Peroxisomal 3-Ketoacyl-Coa Thiolase of Saccharomyces Cerevisiae: Implications for Substrate Binding and Reaction Mechanism

J. Mol. Biol. 273, 714-728 [NCBI_Abstract]

1996

Totrov, M.M., and Abagyan, R.A.
The Contour-Buildup Algorithm To Calculate The Analytical Molecular Surface
J. Struct. Biol. 116, 138-143 [NCBI_Abstract]

Chalikian, T.V., Totrov, M.M., Abagyan, R.A., and Breslauer, K.J.
The Hydration of Globular Proteins As Derived From Volume and Compressibility Measurements: Cross Correlating Thermodynamic and Structural Data
J. Mol. Biol. 260, 588-603 [NCBI_Abstract]

Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B.K., Kuntz, I.D., Abagyan, R., Totrov, M., Janin, J., Cherfils, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M., and James, M.N.G.
Molecular Docking Programs Successfully Predict The Binding of A Beta-Lactamase inhibitory Protein To Tem-1 Beta-Lactamase

Nature Struct. Biol. 3, 233-239 [NCBI_Abstract]

Goodman, A.R., Cardozo, T., Abagyan, R.A., Altmeyer, A., Wisniewski, H.G., and Vilcek, J.
Long Pentraxins: An Emerging Group of Proteins With Diverse Functions
Cytokine & Growth Factor Reviews 7, 191-202 [NCBI_Abstract]

1995

Borchert, T.V., Kishan, K.V.R., Zeelen, J.Ph., Schliebs, W., Thanki, N., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K.
Three New Crystal Structures of Point Mutation Variants of Monotim: Conformational Flexibility of Loop-1, Loop-4 and Loop-8
Structure 3, 669-679 [NCBI_Abstract]

Houbrechts, A., Moreau, B., Abagyan, R., Mainfroid, V., Preaux G., Lamproye, A., Poncin, A., Goormaghtigh, E., Ryusschaert, J.-M., Martial, J.A., and Goraj, K.

Second-Generation Octarellins: Two New De Novo (??)8 Polypeptides Designed For investigating The influence of ?-Residue Packing On The ?/? -Barrel Structure Stability
Protein Engineering 8, 249-259 [NCBI_Abstract]

Cardozo, T., Totrov, M., and Abagyan, R.
Homology Modeling By The Icm Method
Proteins: Structure, Function, and Genetics 403-414 [NCBI_Abstract]

1994

Abagyan, R.A., Frishman, D., and Argos, P.
Recognition of Distantly Related Proteins Through Energy Calculations
Proteins 19, 132-140 [NCBI_Abstract]

Argos, P. and Abagyan, R.A.

The Protein Folding Problem: Finding A Few Minimums in A Near infinite Space
Computers & Chemistry 18, 225-232 [Abs.] - [NCBI_Abstract]

Abagyan, R.A. and Totrov, M.M.
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins
J. Mol. Biol. 235, 983-1002 [NCBI_Abstract]

Borchert, T.V., Abagyan, R.A., Jaenicke, R., and Wierenga, R.K.
Design, Creation, and Characterization of A Stable, Monomeric Triosephosphate Isomerase
Proc. Natl. Acad. Sci. USA 91, 1515-1518 [NCBI_Abstract]

Totrov, M.M. and Abagyan, R.A.
Detailed Ab initio Prediction of Lysozyme-Antibody Complex With 1.6 Accuracy

Nature Structural Biology 1, 259-263 [NCBI_Abstract]

Abagyan, R.A., Totrov, M.M., and Kuznetsov, D.A.
Icm: A New Method For Protein Modeling and Design: Applications To Docking and Structure Prediction From The Distorted Native Conformation
J. Comp. Chem. 15, 488-506

Totrov, M.M. and Abagyan, R.A.
Efficient Parallelization of The Energy, Surface and Derivative Calculations For internal Coordinate Mechanics
J. Comp. Chem. 15, 1105-1112