ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation. - Ruben Abagyan; Maxim Totrov; Dmitry Kuznetsov (J. Comput. Chem., 1994)

Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. - Maxim Totrov; Ruben Abagyan (J. Comput. Chem., 1994)

From fold recognition to flexible docking. - Ruben Abagyan; Serge Batalov; Timothy Cardozo; Maxim Totrov (German Conference on Bioinformatics, 1997)

Derivation of sensitive discrimination potential for virtual ligand screening. - Maxim Totrov; Ruben Abagyan (RECOMB, 1999)

Screened Charge Electrostatic Model in Protein-Protein Docking Simulations. - Juan Fernández-Recio; Maxim Totrov; Ruben Abagyan (Pacific Symposium on Biocomputing, 2002)

Comparative study of several algorithms for flexible ligand docking. - Badry D. Bursulaya; Maxim Totrov; Ruben Abagyan; Charles L. Brooks III (J. Comput. Aided Mol. Des., 2003)

ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. - Vsevolod Katritch; Maxim Totrov; Ruben Abagyan (J. Comput. Chem., 2003)

Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking. - Maxim Totrov (J. Comput. Chem., 2004)

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. - Vsevolod Katritch; Chelsea M. Byrd; Vladimir Tseitin; Dongcheng Dai; Eugene Raush; Maxim Totrov; Ruben Abagyan; Robert Jordan; Dennis E. Hruby (J. Comput. Aided Mol. Des., 2007)

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). - Giovanni Bottegoni; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2008)

Spatial chemical distance based on atomic property fields. - A. V. Grigoryan; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2010)

Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. - Maxim Totrov (BMC Bioinform., 2011)

Docking and scoring with ICM: the benchmarking results and strategies for improvement. - Marco A. C. Neves; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2012)

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. - Manuel Rueda; Maxim Totrov; Ruben Abagyan (J. Chem. Inf. Model., 2012)

FOCUS - Development of a Global Communication and Modeling Platform for Applied and Computational Medicinal Chemists. - Nikolaus Stiefl; Peter Gedeck; Donovan Chin; Peter Hunt; Mika K. Lindvall; Katrin Spiegel; Clayton Springer; Scott Biller; Christoph L. Buenemann; Takanori Kanazawa; Mitsunori Kato; Richard A. Lewis; et al. (J. Chem. Inf. Model., 2015)

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2018)

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2019)

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4. - Polo Chun-Hung Lam; Ruben Abagyan; Maxim Totrov (J. Comput. Aided Mol. Des., 2019)

Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. - Eugene Raush; Ruben Abagyan; Maxim Totrov (J. Chem. Inf. Model., 2022)