M. Totrov

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Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes*

R. Abagyan, J. An, M. Totrov, 2005, Molecular & Cellular Proteomics.

Comprehensive identification of "druggable" protein ligand binding sites.

R. Abagyan, J. An, M. Totrov, 2004, Genome informatics. International Conference on Genome Informatics.

ICM‐DISCO docking by global energy optimization with fully flexible side‐chains

R. Abagyan, J. Fernández-Recio, M. Totrov, 2003, Proteins.

Soft protein–protein docking in internal coordinates

R. Abagyan, J. Fernández-Recio, M. Totrov, 2002, Protein science : a publication of the Protein Society.

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

R. Abagyan, M. Totrov, 1994, Journal of molecular biology.

Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors.

M. Totrov, P. Lam, Christopher J. Monceaux, 2010, Bioorganic & medicinal chemistry letters.

Optimal docking area: A new method for predicting protein–protein interaction sites

R. Abagyan, J. Fernández-Recio, M. Totrov, 2004, Proteins.

Identification of protein-protein interaction sites from docking energy landscapes.

R. Abagyan, J. Fernández-Recio, M. Totrov, 2004, Journal of molecular biology.

Flexible ligand docking to multiple receptor conformations: a practical alternative.

R. Abagyan, M. Totrov, 2008, Current opinion in structural biology.

Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase

J. Cherfils, R. Abagyan, I. Kuntz, 1996, Nature Structural Biology.

Prediction of the binding energy for small molecules, peptides and proteins

Ruben Abagyan, Maxim Totrov, Matthieu Schapira, 1999, Journal of molecular recognition : JMR.

A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening.

M. Totrov, M. H. Howard, T. Cenizal, 2004, Journal of medicinal chemistry.

Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search

R Abagyan, R. Abagyan, S. Batalov, 1997, Proteins.

Nuclear hormone receptor targeted virtual screening.

Ruben Abagyan, Maxim Totrov, Matthieu Schapira, 2003, Journal of medicinal chemistry.

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.

Ruben Abagyan, Maxim Totrov, Irina Kufareva, 2009, Journal of medicinal chemistry.

Flexible protein–ligand docking by global energy optimization in internal coordinates

R Abagyan, R. Abagyan, M. Totrov, 1997, Proteins.

Homology modeling by the ICM method

R Abagyan, R. Abagyan, M. Totrov, 1995, Proteins.

High-throughput docking for lead generation.

R Abagyan, R. Abagyan, M. Totrov, 2001, Current opinion in chemical biology.

Voltage-Sensitive Potassium Kv2 Channels as New Targets for Insecticides

J. Bloomquist, M. Totrov, P. Carlier, 2014 .

Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy

Ruben Abagyan, Maxim Totrov, R. Abagyan, 1994, Nature Structural Biology.

Vacuuming the Periplasm

M. Totrov, O. Lomovskaya, 2005, Journal of bacteriology.

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

R. Abagyan, M. Totrov, Y. A. Arnautova, 2015, Journal of chemical theory and computation.

Acetylcholinesterase of the sand fly, Phlebotomus papatasi (Scopoli): construction, expression and biochemical properties of the G119S orthologous mutant

J. Bloomquist, M. Totrov, P. Carlier, 2014, Parasites & Vectors.

Spectrum of Beta-Lactamase Inhibition by the Cyclic Boronate QPX7728, an Ultrabroad-Spectrum Beta-Lactamase Inhibitor of Serine and Metallo-Beta-Lactamases: Enhancement of Activity of Multiple Antibiotics against Isogenic Strains Expressing Single Beta-Lactamases

M. Totrov, M. Dudley, Dongxu Sun, 2020, Antimicrobial Agents and Chemotherapy.

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

R. Abagyan, M. Orozco, M. Totrov, 2013, BMC Structural Biology.

Induction of neutralizing antibodies in rhesus macaques using V3 mimotope peptides.

N. Haigwood, S. Zolla-Pazner, M. Gorny, 2016, Vaccine.

Structure/Function Studies Involving the V3 Region of the HIV-1 Envelope Delineate Multiple Factors That Affect Neutralization Sensitivity

S. Zolla-Pazner, M. Nussenzweig, M. Totrov, 2015, Journal of Virology.

Differential induction of anti-V3 crown antibodies with cradle- and ladle-binding modes in response to HIV-1 envelope vaccination.

N. Haigwood, S. Zolla-Pazner, M. Gorny, 2017, Vaccine.

Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120.

S. Zolla-Pazner, M. Gorny, M. Totrov, 2011, Structure.

Neurotoxicology of bis(n)-tacrines on Blattella germanica and Drosophila melanogaster acetylcholinesterase.

J. Bloomquist, M. Totrov, P. Lam, 2013, Archives of insect biochemistry and physiology.

Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector Anopheles gambiae

M. Totrov, P. Lam, P. Carlier, 2018, Insect science.

Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease

M. Totrov, A. Gudkov, S. Korolev, 2021, Nucleic acids research.

Pocketome: Comprehensive Identification and Classification of Ligand-Binding Envelopes Authors:

R. Abagyan, J. An, M. Totrov, 2004 .

Multimeric Epitope-Scaffold HIV Vaccines Target V1V2 and Differentially Tune Polyfunctional Antibody Responses.

N. Haigwood, S. Zolla-Pazner, M. Totrov, 2019, Cell reports.

QPX7728, An Ultra-Broad-Spectrum B-Lactamase Inhibitor for Intravenous and Oral Therapy: Overview of Biochemical and Microbiological Characteristics

M. Totrov, M. Dudley, Dongxu Sun, 2021, Frontiers in Microbiology.

Select Small Core Structure Carbamates Exhibit High Contact Toxicity to “Carbamate-Resistant” Strain Malaria Mosquitoes, Anopheles gambiae (Akron)

J. Bloomquist, M. Totrov, P. Lam, 2012, PloS one.

The use of the magnetic field effect for studying a chemiluminescent chemical reaction in aqueous solution. Reaction rate constants and lifetimes of intermediate molecules

M. Totrov, M. Triebel, E. Frankevich, 1993 .

Phase-on-frequency characteristics of the magnetic field effect for studying the mechanism of the branching chemiluminescent reaction of luminol

M. Totrov, M. Triebel, E. Frankevich, 1993 .

Anti-V2 Antibody Deficiency in Individuals Infected With HIV-1

S. Zolla-Pazner, M. Gorny, M. Totrov, 2018, bioRxiv.

Discovery of Species-selective and Resistance-breaking Anticholinesterase Insecticides for the Malaria Mosquito.

J. Bloomquist, M. Totrov, P. Carlier, 2017, Current medicinal chemistry.

Structural genomics for drug design against the pathogen Coxiella burnetii

Maxim Totrov, Zhong-Ke Yao, M. Totrov, 2015, Proteins.

3-Oxoisoxazole-2(3H)-carboxamides and isoxazol-3-yl carbamates: Resistance-breaking acetylcholinesterase inhibitors targeting the malaria mosquito, Anopheles gambiae.

J. Bloomquist, M. Totrov, P. Lam, 2015, Bioorganic & medicinal chemistry.

Comparative study of several algorithms for flexible ligand docking

Ruben Abagyan, Maxim Totrov, Charles L. Brooks, 2003, J. Comput. Aided Mol. Des..

Re-engineering aryl methylcarbamates to confer high selectivity for inhibition of Anopheles gambiae versus human acetylcholinesterase.

J. Bloomquist, M. Totrov, P. Lam, 2012, Bioorganic & medicinal chemistry letters.

Enantiopure Benzofuran-2-carboxamides of 1-Aryltetrahydro-β-carbolines Are Potent Antimalarials In Vitro.

M. Cassera, E. F. Merino, J. H. Butler, 2022, ACS medicinal chemistry letters.

Inhibitor profile of bis(n)-tacrines and N-methylcarbamates on acetylcholinesterase from Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi.

Fan Tong, J. Bloomquist, M. Totrov, 2013, Pesticide biochemistry and physiology.

ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov, 1994, J. Comput. Chem..

Mosquito Acetylcholinesterase as a Target for Novel Phenyl-Substituted Carbamates

J. Bloomquist, M. Totrov, P. Carlier, 2019, International journal of environmental research and public health.

Waltzing transporters and 'the dance macabre' between humans and bacteria

M. Totrov, H. Zgurskaya, W. Watkins, 2007, Nature Reviews Drug Discovery.

Docking and scoring with ICM: the benchmarking results and strategies for improvement

Ruben Abagyan, Maxim Totrov, Marco A. C. Neves, 2012, Journal of Computer-Aided Molecular Design.

Discovery of Cyclic Boronic Acid QPX7728, an Ultra-broad-spectrum Inhibitor of Serine and Metallo Beta-lactamases.

M. Totrov, Yu Chen, K. R. Reddy, 2020, Journal of medicinal chemistry.

Discovery of a Cyclic Boronic Acid β-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases.

M. Totrov, K. R. Reddy, J. Loutit, 2015, Journal of medicinal chemistry.

Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition

M. Totrov, Yu Chen, O. Lomovskaya, 2020, Antimicrobial Agents and Chemotherapy.

Broad-spectrum cyclic boronate β-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.

M. Totrov, S. Hecker, O. Lomovskaya, 2022, Bioorganic & medicinal chemistry.

In Vitro Activity of the Ultra-Broad-Spectrum Beta-Lactamase Inhibitor QPX7728 in Combination with Meropenem against Clinical Isolates of Carbapenem-Resistant Acinetobacter baumannii

M. Totrov, M. Dudley, Dongxu Sun, 2020, Antimicrobial Agents and Chemotherapy.

Biochemical Characterization of QPX7728, a New Ultrabroad-Spectrum Beta-Lactamase Inhibitor of Serine and Metallo-Beta-Lactamases

M. Totrov, O. Lomovskaya, Ruslan Tsivkovski, 2020, Antimicrobial Agents and Chemotherapy.

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

Ruben Abagyan, Maxim Totrov, Matthieu Schapira, 2002, BMC Structural Biology.

Towards a species-selective acetylcholinesterase inhibitor to control the mosquito vector of malaria, Anopheles gambiae.

J. Bloomquist, M. Totrov, P. Lam, 2008, Chemico-biological interactions.

Small Molecule Inhibitor of Neutrophil Elastase Restores Impaired Production of Human Myeloid Cells Observed in Severe Congenital Neutropenia.

R. Abagyan, M. Totrov, D. Dale, 2007 .

Expression of the adenovirus receptor and its interaction with the fiber knob.

R. Abagyan, J. Frisén, M. Totrov, 2000, Experimental cell research.

Aryl methylcarbamates: potency and selectivity towards wild-type and carbamate-insensitive (G119S) Anopheles gambiae acetylcholinesterase, and toxicity to G3 strain An. gambiae.

J. Bloomquist, M. Totrov, P. Lam, 2013, Chemico-biological interactions.

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

Ruben Abagyan, Maxim Totrov, Dennis E. Hruby, 2007, J. Comput. Aided Mol. Des..

Biological Studies and Target Engagement of the 2- C-Methyl-d-Erythritol 4-Phosphate Cytidylyltransferase (IspD)-Targeting Antimalarial Agent (1 R,3 S)-MMV008138 and Analogs.

M. Cassera, E. F. Merino, J. H. Butler, 2017, ACS Infectious Diseases.

Computer applications for prediction of protein-protein interactions and rational drug design.

Solène Grosdidier, Juan Fernández-Recio, Max Totrov, 2009, Advances and applications in bioinformatics and chemistry : AABC.

Protein-RNA Docking Using ICM.

Ruben Abagyan, Maxim Totrov, R. Abagyan, 2018, Journal of chemical theory and computation.

Rationally Designed Immunogens Targeting HIV-1 gp120 V1V2 Induce Distinct Conformation-Specific Antibody Responses in Rabbits

S. Zolla-Pazner, M. Totrov, Xueling Wu, 2016, Journal of Virology.

PIER: Protein interface recognition for structural proteomics

Ruben Abagyan, Maxim Totrov, Irina Kufareva, 2007, Proteins.

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.

R Abagyan, I D Kuntz, M Sternberg, 1996, Nature structural biology.

Select β- and γ-branched 1-alkylpyrazol-4-yl methylcarbamates exhibit high selectivity for inhibition of Anopheles gambiae versus human acetylcholinesterase.

J. Bloomquist, M. Totrov, P. Carlier, 2018, Pesticide biochemistry and physiology.

Difluoromethyl ketones: Potent inhibitors of wild type and carbamate-insensitive G119S mutant Anopheles gambiae acetylcholinesterase.

J. Bloomquist, M. Totrov, P. Carlier, 2015, Bioorganic & medicinal chemistry letters.

STRUCTURAL STUDIES OF Anopheles gambiae ACETYLCHOLINESTERASE PROVIDE INSIGHT TOWARDS IMPROVED INSECTICIDES FOR MALARIA VECTOR CONTROL

M. Totrov, P. Carlier, Lixuan Liu, 2018 .

Plasticity and Epitope Exposure of the HIV-1 Envelope Trimer

S. Zolla-Pazner, M. Totrov, A. Fox, 2017, Journal of Virology.

A New Method for Publishing Three-Dimensional Content

Ruben Abagyan, Brian D. Marsden, Eugene Raush, 2009, PloS one.

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking

Ruben Abagyan, Maxim Totrov, Matthieu Schapira, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure

Ruben Abagyan, Maxim Totrov, R. Abagyan, 1999 .

Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking

Maxim Totrov, M. Totrov, 2004, J. Comput. Chem..

Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.

R. Abagyan, S. Zolla-Pazner, M. Gorny, 2010, Virology.

Functional conservation of Rel binding sites in drosophilid genomes.

J. Ragoussis, R. Copley, M. Totrov, 2007, Genome research.

Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure

S. Zolla-Pazner, M. Gorny, M. Totrov, 2011, PLoS ONE.

ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field

Ruben Abagyan, Maxim Totrov, Vsevolod Katritch, 2003, J. Comput. Chem..

Computational studies on protein-ligand docking.

Maxim Totrov, M. Totrov, 1999 .

Functional Antibody Response Against V1V2 and V3 of HIV gp120 in the VAX003 and VAX004 Vaccine Trials

N. Haigwood, S. Zolla-Pazner, M. Totrov, 2018, Scientific Reports.

An HIV Vaccine Targeting the V2 Region of the HIV Envelope Induces a Highly Durable Polyfunctional Fc-Mediated Antibody Response in Rhesus Macaques

N. Haigwood, S. Zolla-Pazner, M. Totrov, 2020, Journal of Virology.

Rationally Designed Vaccines Targeting the V2 Region of HIV-1 gp120 Induce a Focused, Cross-Clade-Reactive, Biologically Functional Antibody Response

S. Zolla-Pazner, M. Totrov, X. Kong, 2016, Journal of Virology.

Cross-Clade HIV-1 Neutralizing Antibodies Induced with V3-Scaffold Protein Immunogens following Priming with gp120 DNA

S. Zolla-Pazner, M. Totrov, A. Nadas, 2011, Journal of Virology.

Conserved structural elements in the V3 crown of HIV-1 gp120

Timothy Cardozo, Maxim Totrov, Susan Zolla-Pazner, 2010, Nature Structural &Molecular Biology.

Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4

Ruben Abagyan, Maxim Totrov, Polo C.-H. Lam, 2019, Journal of Computer-Aided Molecular Design.

IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance

M. Herlyn, M. Totrov, M. Murphy, 2020, Nature.

IspH inhibitors kill Gram-negative bacteria and mobilize immune clearance

M. Herlyn, M. Totrov, M. Murphy, 2020, Nature.

Toxicology of potassium channel‐directed compounds in mosquitoes

J. Bloomquist, M. Totrov, P. Carlier, 2017, Neurotoxicology.

HIV p24 as Scaffold for Presenting Conformational HIV Env Antigens

M. Totrov, F. Buonaguro, L. Buonaguro, 2012, PloS one.

Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

Maxim Totrov, M. Totrov, 2007, Chemical biology & drug design.

The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data.

R Abagyan, R. Abagyan, M. Totrov, 1996, Journal of molecular biology.

Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3

Ruben Abagyan, Maxim Totrov, Polo Chun-Hung Lam, 2018, Journal of Computer-Aided Molecular Design.

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ruben Abagyan, Maxim Totrov, Polo Chun-Hung Lam, 2017, Journal of Computer-Aided Molecular Design.

Estimated Secondary Structure Propensities within V1/V2 Region of HIV gp120 Are an Important Global Antibody Neutralization Sensitivity Determinant

M. Totrov, 2014, PloS one.

Development of a new physics‐based internal coordinate mechanics force field and its application to protein loop modeling

Maxim Totrov, R. Abagyan, M. Totrov, 2011, Proteins.

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, M. Totrov, 2011, BMC Bioinformatics.

Malaria Box-Inspired Discovery of N-Aminoalkyl-β-carboline-3-carboxamides, a Novel Orally Active Class of Antimalarials.

M. Cassera, M. Totrov, P. Carlier, 2022, ACS medicinal chemistry letters.

1 CROSS-CLADE HIV-1 NEUTRALIZING ANTIBODIES INDUCED WITH 1 V 3-SCAFFOLD PROTEIN IMMUNOGENS FOLLOWING PRIMING WITH gp 120 DNA 2 3 Running Title : Vaccine-induced HIV neutralizing antibodies 4 5

S. Zolla-Pazner, M. Totrov, A. Nadas, 2011 .

Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.

R Abagyan, R. Abagyan, M. Totrov, 2001, Biopolymers.

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

Ruben Abagyan, Maxim Totrov, Irina Kufareva, 2008, J. Comput. Aided Mol. Des..

Interactive JIMD articles using the iSee concept: turning a new page on structural biology data

Ruben Abagyan, Maxim Totrov, Brian D. Marsden, 2011, Journal of Inherited Metabolic Disease.

Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches

Chelsea M. Byrd, R. Abagyan, M. Totrov, 2007, J. Comput. Aided Mol. Des..

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping.

Ruben Abagyan, R. Abagyan, M. Totrov, 2014, Future medicinal chemistry.

Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules

R. Abagyan, M. Totrov, E. Raush, 2022, J. Chem. Inf. Model..

Bivalent Carbamates as Novel Control Agents of the Malaria Mosquito, Anopheles gambiae.

J. Bloomquist, M. Totrov, P. Lam, 2016, Chimia.

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

Ruben Abagyan, Maxim Totrov, Manuel Rueda, 2012, J. Chem. Inf. Model..

Derivation of sensitive discrimination potential for virtual ligand screening

Ruben Abagyan, Maxim Totrov, R. Abagyan, 1999, RECOMB.

The contour-buildup algorithm to calculate the analytical molecular surface.

R Abagyan, R. Abagyan, M. Totrov, 1996, Journal of structural biology.

Spatial chemical distance based on atomic property fields

Ruben Abagyan, Maxim Totrov, A. V. Grigoryan, 2010, J. Comput. Aided Mol. Des..

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

R. Abagyan, G. Bottegoni, M. Totrov, 2008, J. Comput. Aided Mol. Des..

Functional Antibody Response Against V1V2 and V3 of HIV gp120 in the VAX003 and VAX004 Vaccine Trials

N. Haigwood, S. Zolla-Pazner, M. Totrov, 2018, Scientific Reports.

Advances and Applications in Bioinformatics and Chemistry Dovepress Open Access to Scientific and Medical Research Open Access Full Text Article Dovepress Computer Applications for Prediction of Protein–protein Interactions and Rational Drug Design

J. Fernández-Recio, M. Totrov, S. Grosdidier, 2022 .

Contact area difference (CAD): a robust measure to evaluate accuracy of protein models.

M. Totrov, R A Abagyan, M M Totrov, 1997, Journal of molecular biology.

Vacuuming the Periplasm

M. Totrov, O. Lomovskaya, 2005, Journal of bacteriology.

New boronate drugs and evolving NDM-mediated beta-lactam resistance

M. Castanheira, M. Totrov, O. Lomovskaya, 2023, Antimicrobial agents and chemotherapy.

In vitro potency of xeruborbactam in combination with multiple β-lactam antibiotics in comparison with other β-lactam/β-lactamase inhibitor (BLI) combinations against carbapenem-resistant and extended-spectrum β-lactamase-producing Enterobacterales

M. Castanheira, M. Totrov, Kirk J. Nelson, 2023, Antimicrobial agents and chemotherapy.