| |

Publications


Selected peer-reviewed publications by MolSoft's scientists, developers, and customers (from 2010 onwards).

ICM Methods | Virtual Screening | Molecular Modeling

TitleAuthorsJournalYearPubMedNotes
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules Raush E, Abagyan R, Totrov MJ Chem Inf Model202236456533 A graph-convolutional neural network (GCNN)-based method for learning and prediction of statistical torsional profiles (STP) in small organic molecules based on the experimental X-ray structure data.
Synthon-based ligand discovery in virtual libraries of over 11 billion compounds Sadybekov et alNature202234912117A synthon based approach for giga sized library screening.
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4 Lam P, Abagyan R, Totrov MJ. Comput Aided Mol Des.201931598897MolSoft ICM outperformed all other methods for macrocycle docking and screening in the D3R Grand Challenge 4.
Protein-RNA Docking Using ICM. Arnautova YA, Abagyan R, Totrov MJ Chem Theory Comput. 2018201830016588Description of MolSoft's ICM Protein RNA docking method.
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3. Lam P, Abagyan R, Totrov MJ Comput Aided Mol Des. 2018201830094533MolSoft's ICM software ranked in first place for average RMSD docking accuracy in the D3R Grand Challenge 3 Read more here.
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach.Lam P, Abagyan R, Totrov MJ Comput Aided Mol Des. 2018201828887659MolSoft's ICM software ranked in first place for average RMSD docking accuracy in the 2016-17 Drug Design challenge competition http://drugdesigndata.org/ (D3R)
SMN2 splice modulators enhance U1-pre-mRNA association and rescue SMA mice.Palacino et alNat Chem Biol. 2015 201526030728 RNA Ligand Guided Modeling Success Story by Novartis
Discovery of a Natural Product-Like iNOS Inhibitor by Molecular Docking with Potential Neuroprotective Effects In VivoZhong HJ, Liu LJ, Chong CM, Lu L, Wang M, Chan DS, Chan PW, Lee SM, Ma DL, Leung CH.PLoS One. 2014201424690920
Structure-based discovery of a small non-peptidic Neuropilins antagonist exerting in vitro and in vivo anti-tumor activity on breast cancer model.Borriello L, Montes M, Lepelletier Y, Leforban B, Liu WQ, Demange L, Delhomme B, Pavoni S, Jarray R, Boucher JL, Dufour S, Hermine O, Garbay C, Hadj-Slimane R, Raynaud F.Cancer Lett. 2014201424752068
Discovery of novel ligands for mouse olfactory receptor MOR42-3 using an in silico screening approach and in vitro validation.Bavan S, Sherman B, Luetje CW, Abaffy T.PLoS One. 2014201424637889
Identification and Characterization of Small Molecules That Inhibit Nonsense-Mediated RNA Decay and Suppress Nonsense p53 Mutations.Martin L, Grigoryan A, Wang D, Wang J, Breda L, Rivella S, Cardozo T, Gardner LB.Cancer Res. 2014201424662918
Structure-based Design, Synthesis, and Biological Evaluation of Insatin Derivatives as Potential Glycosyltransferase Inhibitors.Wang Y, Chan FY, Sun N, Lui HK, So PK, Yan SC, Chan KF, Chiou J, Chen S, Abagyan R, Leung YC, Wong KY.Chem Biol Drug Des. 2014201424890564
Rational Design of Berberine-Based FtsZ Inhibitors with Broad-Spectrum Antibacterial Activity.Sun N, Chan FY, Lu YJ, Neves MA, Lui HK, Wang Y, Chow KY, Chan KF, Yan SC, Leung YC, Abagyan R, Chan TH, Wong KY.PLoS One. 2014201424824618
Identification of novel serotonin transporter compounds by virtual screening.Gabrielsen M, Kurczab R, Siwek A, Wolak M, Ravna AW, Kristiansen K, Kufareva I, Abagyan R, Nowak G, Chilmonczyk Z, Sylte I, Bojarski AJ.J Chem Inf Model. 2014201424521202
A general method for site specific fluorescent labeling of recombinant chemokines.Kawamura T, Stephens B, Qin L, Yin X, Dores MR, Smith TH, Grimsey N, Abagyan R, Trejo J, Kufareva I, Fuster MM, Salanga CL, Handel TM.PLoS One. 2014201424489642
PeptiSite: a structural database of peptide binding sites in 4D.Acharya C, Kufareva I, Ilatovskiy AV, Abagyan R.Biochem Biophys Res Commun. 2014201424406170
In silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species.McRobb FM, Sahag??n V, Kufareva I, Abagyan R.Environ Sci Technol. 2014201424392850
The second extracellular loop of the adenosine A1 receptor mediates activity of allosteric enhancers.Kennedy DP, McRobb FM, Leonhardt SA, Purdy M, Figler H, Marshall MA, Chordia M, Figler R, Linden J, Abagyan R, Yeager M.Mol Pharmacol. 2014201424217444
Estimated secondary structure propensities within V1/V2 region of HIV gp120 are an important global antibody neutralization sensitivity determinant.Totrov M.PLoS One. 2014201424705879
High-throughput virtual screening identifies novel N'-(1-phenylethylidene)-benzohydrazides as potent, specific, and reversible LSD1 inhibitors.Sorna V, Theisen ER, Stephens B, Warner SL, Bearss DJ, Vankayalapati H, Sharma S.J Med Chem. 20132013 24237195
Computational Evidence for the Reactivation Process of Human Acetylcholinesterase Inhibited by Carbamates.Matos KS, da Cunha EF, Abagyan R, Ramalho TC.Comb Chem High Throughput Screen. 2013201324344993
BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.Rueda M, Orozco M, Totrov M, Abagyan R.BMC Struct Biol. 2013201324330655
Homology modeling and ligand docking of Mitogen-activated protein kinase-activated protein kinase 5 (MK5).Lindin I, Wuxiuer Y, Kufareva I, Abagyan R, Moens U, Sylte I, Ravna AW.Theor Biol Med Model. 2013201324034446
Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors.Lane JR, Chubukov P, Liu W, Canals M, Cherezov V, Abagyan R, Stevens RC, Katritch V.Mol Pharmacol. 2013201324021214
Identification of a new class of FtsZ inhibitors by structure-based design and in vitro screening.Chan FY, Sun N, Neves MA, Lam PC, Chung WH, Wong LK, Chow HY, Ma DL, Chan PH, Leung YC, Chan TH, Abagyan R, Wong KY.J Chem Inf Model. 2013201323848971
Molecular basis for benzodiazepine agonist action at the type 1 cholecystokinin receptor.Harikumar KG, Cawston EE, Lam PC, Patil A, Orry A, Henke BR, Abagyan R, Christopoulos A, Sexton PM, Miller LJ.J Biol Chem. 2013201323754289
Beta-amyloid peptides undergo regulated co-secretion with neuropeptide and catecholamine neurotransmitters.Toneff T, Funkelstein L, Mosier C, Abagyan A, Ziegler M, Hook V.Peptides. 2013201323747840
Viral infection controlled by a calcium-dependent lipid-binding module in ALIX.Bissig C, Lenoir M, Velluz MC, Kufareva I, Abagyan R, Overduin M, Gruenberg J.Dev Cell. 2013201323664863
A novel approach to quantify G-protein-coupled receptor dimerization equilibrium using bioluminescence resonance energy transfer.Kufareva I, Stephens B, Gilliland CT, Wu B, Fenalti G, Hamel D, Stevens RC, Abagyan R, Handel TM.Methods Mol Biol. 2013201323625495
Predicting p Ka values from EEM atomic charges.Va?ekov?? RS, Geidl S, Ionescu CM, Sk?ehota O, Bouchal T, Sehnal D, Abagyan R, Ko?a J.J Cheminform. 2013201323574978
Synthesis, antidepressant evaluation and docking studies of long-chain alkylnitroquipazines as serotonin transporter inhibitors.Gabrielsen M, Wo?osewicz K, Zawadzka A, Kossakowski J, Nowak G, Wolak M, Stachowicz K, Siwek A, Ravna AW, Kufareva I, Kozerski L, Bednarek E, Sitkowski J, Bocian W, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z.Chem Biol Drug Des. 2013201323574807
Lapatinib-binding protein kinases in the African trypanosome: identification of cellular targets for kinase-directed chemical scaffolds.Katiyar S, Kufareva I, Behera R, Thomas SM, Ogata Y, Pollastri M, Abagyan R, Mensa-Wilmot K.PLoS One. 2013201323437089
The GPCR Network: a large-scale collaboration to determine human GPCR structure and function.Stevens RC, Cherezov V, Katritch V, Abagyan R, Kuhn P, Rosen H, W?Șthrich K.Nat Rev Drug Discov. 2013201323237917
Molecular mechanisms deployed by virally encoded G protein-coupled receptors in human diseases.Montaner S, Kufareva I, Abagyan R, Gutkind JS.Annu Rev Pharmacol Toxicol. 2013201323092247
Inhibitor profile of bis(n)-tacrines and N-methylcarbamates on acetylcholinesterase from Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi.Swale DR, Tong F, Temeyer KB, Li A, Lam PC, Totrov MM, Carlier PR, P??rez de Le??n AA, Bloomquist JR.Pestic Biochem Physiol. 2013201324187393
Neurotoxicology of bis(n)-tacrines on Blattella germanica and Drosophila melanogaster acetylcholinesterase.Mutunga JM, Boina DR, Anderson TD, Bloomquist JR, Carlier PR, Wong DM, Lam PC, Totrov MM.Arch Insect Biochem Physiol. 2013201323740645
Aryl methylcarbamates: potency and selectivity towards wild-type and carbamate-insensitive (G119S) Anopheles gambiae acetylcholinesterase, and toxicity to G3 strain An. gambiae.Wong DM, Li J, Lam PC, Hartsel JA, Mutunga JM, Totrov M, Bloomquist JR, Carlier PR.Chem Biol Interact. 2013201322989775
Specific small molecule inhibitors of Skp2-mediated p27 degradation.Wu L, Grigoryan AV, Li Y, Hao B, Pagano M, Cardozo TJ.Chem Biol. 2012201223261596
Compound activity prediction using models of binding pockets or ligand properties in 3D.Kufareva I, Chen YC, Ilatovskiy AV, Abagyan R.Curr Top Med Chem. 2012201223116466
Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping.Dong M, Xu X, Ball AM, Makhoul JA, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ.FASEB J. 2012201222964305
Small molecule inhibitors of Bacillus anthracis protective antigen proteolytic activation and oligomerization.Wein AN, Williams BN, Liu S, Ermolinsky B, Provenzano D, Abagyan R, Orry A, Leppla SH, Peredelchuk M.J Med Chem. 2012201222954387
ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.Rueda M, Totrov M, Abagyan R.J Chem Inf Model. 2012201222947092Induced Fit Docking
A metal-based inhibitor of tumor necrosis factor-?€.Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DS, Ma VP, Abagyan R, Wong CY, Ma DL.Angew Chem Int Ed Engl. 2012201222807261
Docking and scoring with ICM: the benchmarking results and strategies for improvement.Neves MA, Totrov M, Abagyan R.J Comput Aided Mol Des. 2012201222569591ICM Docking Benchmark
Validation of the AmpC ??-lactamase binding site and identification of inhibitors with novel scaffolds.Chan FY, Neves MA, Sun N, Tsang MW, Leung YC, Chan TH, Abagyan R, Wong KY.J Chem Inf Model. 2012201222559726
Unusual arginine formations in protein function and assembly: rings, strings, and stacks.Neves MA, Yeager M, Abagyan R.J Phys Chem B. 2012201222497303
Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening.Tosh DK, Phan K, Gao ZG, Gakh AA, Xu F, Deflorian F, Abagyan R, Stevens RC, Jacobson KA, Katritch V.J Med Chem. 2012201222486652
Molecular basis for binding and subtype selectivity of 1,4-benzodiazepine antagonist ligands of the cholecystokinin receptor.Cawston EE, Lam PC, Harikumar KG, Dong M, Ball AM, Augustine ML, Akg?Șn E, Portoghese PS, Orry A, Abagyan R, Sexton PM, Miller LJ.J Biol Chem. 2012201222467877
Novel cGMP efflux inhibitors identified by virtual ligand screening (VLS) and confirmed by experimental studies.Sager G, ??rvoll E??, Lysaa RA, Kufareva I, Abagyan R, Ravna AW.J Med Chem. 2012201222380603
Preparation and refinement of model protein-ligand complexes.Orry AJ, Abagyan R.Methods Mol Biol. 2012201222323230
Methods of protein structure comparison.Kufareva I, Abagyan R.Methods Mol Biol. 2012201222323224
Ligand-guided receptor optimization.Katritch V, Rueda M, Abagyan R.Methods Mol Biol. 2012201222323222
Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.Jaro?czyk M, Wo?osewicz K, Gabrielsen M, Nowak G, Kufareva I, Mazurek AP, Ravna AW, Abagyan R, Bojarski AJ, Sylte I, Chilmonczyk Z.Eur J Med Chem. 2012201222309909
Computational chemistry in 25 years.Abagyan R.J Comput Aided Mol Des. 2012201222160588
Pocketome: an encyclopedia of small-molecule binding sites in 4D.Kufareva I, Ilatovskiy AV, Abagyan R.Nucleic Acids Res. 2012201222080553Pocketome
Molecular mechanism of serotonin transporter inhibition elucidated by a new flexible docking protocol.Gabrielsen M, Kurczab R, Ravna AW, Kufareva I, Abagyan R, Chilmonczyk Z, Bojarski AJ, Sylte I.Eur J Med Chem. 2012201222071255
HIV p24 as scaffold for presenting conformational HIV Env antigens.Tagliamonte M, Marasco D, Ruggiero A, De Stradis A, Tornesello ML, Totrov M, Buonaguro FM, Buonaguro L.PLoS One. 2012201222912852
Re-engineering aryl methylcarbamates to confer high selectivity for inhibition of Anopheles gambiae versus human acetylcholinesterase.Hartsel JA, Wong DM, Mutunga JM, Ma M, Anderson TD, Wysinski A, Islam R, Wong EA, Paulson SL, Li J, Lam PC, Totrov MM, Bloomquist JR, Carlier PR.Bioorg Med Chem Lett. 2012201222738634
Loop simulations.Totrov M.Methods Mol Biol. 2012201222323223
Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble.Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM.Nat Chem Biol. 2011201121706033 RNA Dde novo inhibitor success story.
Tyrosine phosphorylation of the G?€-interacting protein GIV promotes activation of phosphoinositide 3-kinase during cell migration.Lin C, Ear J, Pavlova Y, Mittal Y, Kufareva I, Ghassemian M, Abagyan R, Garcia-Marcos M, Ghosh P.Sci Signal. 2011201121954290
Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model.Bordner AJ, Zorman B, Abagyan R.J Comput Aided Mol Des. 2011201121904908
GPCR agonist binding revealed by modeling and crystallography.Katritch V, Abagyan R.Trends Pharmacol Sci. 2011201121903279GPCR Modeling Success Story
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R; GPCR Dock 2010 participants.Structure. 2011201121827947GPCR Modeling Assessment
Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes.Svobodov?? Varekov?? R, Geidl S, Ionescu CM, Skrehota O, Kudera M, Sehnal D, Bouchal T, Abagyan R, Huber HJ, Koca J.J Chem Inf Model. 2011201121761919
Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.Teplova M, Malinina L, Darnell JC, Song J, Lu M, Abagyan R, Musunuru K, Teplov A, Burley SK, Darnell RB, Patel DJ.Structure. 2011201121742260
Structure of the human histamine H1 receptor complex with doxepin.Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, Iwata S.Nature. 2011201121697825
Systematic exploitation of multiple receptor conformations for virtual ligand screening.Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A.PLoS One. 2011201121625529Induced Fit Docking
Molecular basis of secretin docking to its intact receptor using multiple photolabile probes distributed throughout the pharmacophore.Dong M, Lam PC, Pinon DI, Hosohata K, Orry A, Sexton PM, Abagyan R, Miller LJ.J Biol Chem. 2011201121566140
Interactive JIMD articles using the iSee concept: turning a new page on structural biology data.Lee WH, Yue WW, Raush E, Totrov M, Abagyan R, Oppermann U, Marsden BD.J Inherit Metab Dis. 2011201121509537ActiveICM
Refinement of glucagon-like peptide 1 docking to its intact receptor using mid-region photolabile probes and molecular modeling.Miller LJ, Chen Q, Lam PC, Pinon DI, Sexton PM, Abagyan R, Dong M.J Biol Chem. 2011201121454562
In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening.Dey R, Chen L.J Biomol Struct Dyn. 2011201121294583
A natural product-like inhibitor of NEDD8-activating enzyme.Leung CH, Chan DS, Yang H, Abagyan R, Lee SM, Zhu GY, Fong WF, Ma DL.Chem Commun (Camb). 2011201121240405
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.Arnautova YA, Abagyan RA, Totrov M.Proteins. 2011201121069716ICM Force Field
Structure based prediction of subtype-selectivity for adenosine receptor antagonists.Katritch V, Kufareva I, Abagyan R.Neuropharmacology. 2011201120637786
Human anti-V3 HIV-1 monoclonal antibodies encoded by the VH5-51/VL lambda genes define a conserved antigenic structure.Gorny MK, Sampson J, Li H, Jiang X, Totrov M, Wang XH, Williams C, O'Neal T, Volsky B, Li L, Cardozo T, Nyambi P, Zolla-Pazner S, Kong XP.PLoS One. 2011201122164215
Cross-clade HIV-1 neutralizing antibodies induced with V3-scaffold protein immunogens following priming with gp120 DNA.Zolla-Pazner S, Kong XP, Jiang X, Cardozo T, N?­das A, Cohen S, Totrov M, Seaman MS, Wang S, Lu S.J Virol. 2011201121795338
Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors.Monceaux CJ, Hirata-Fukae C, Lam PC, Totrov MM, Matsuoka Y, Carlier PR.Bioorg Med Chem Lett. 2011201121621412
Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120.Spurrier B, Sampson JM, Totrov M, Li H, O'Neal T, Williams C, Robinson J, Gorny MK, Zolla-Pazner S, Kong XP.Structure. 2011201121565703
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites.Totrov M.BMC Bioinformatics. 2011201121342566Atomic Property Fields
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC.Science. 2010201020929726
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.Rueda M, Katritch V, Raush E, Abagyan R.Bioinformatics. 2010201020871105
Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography.Wacker D, Fenalti G, Brown MA, Katritch V, Abagyan R, Cherezov V, Stevens RC.J Am Chem Soc. 2010201020669948
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S.Virology. 2010201020663531
The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening.Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE, Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A.J Med Chem. 2010201020575553
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor.Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Larocca C, Saldanha SA, Abagyan R, Sun Y, Meyers DJ, Marmorstein R, Mahadevan LC, Alani RM, Cole PA.Chem Biol. 2010201020534345Screened 500K compounds and selected 194 for experimental testing resulting in 3 inhibitors which had specificity.
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles.Park SJ, Kufareva I, Abagyan R.J Comput Aided Mol Des. 2010201020455005
Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention.Cheltsov AV, Aoyagi M, Aleshin A, Yu EC, Gilliland T, Zhai D, Bobkov AA, Reed JC, Liddington RC, Abagyan R.J Med Chem. 2010201020441222
Structure-based discovery of natural-product-like TNF-?€ inhibitors.Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL.Angew Chem Int Ed Engl. 2010201020235259
Spatial chemical distance based on atomic property fields.Grigoryan AV, Kufareva I, Totrov M, Abagyan RA.J Comput Aided Mol Des. 2010201020229197
Secretin occupies a single protomer of the homodimeric secretin receptor complex: insights from photoaffinity labeling studies using dual sites of covalent attachment.Dong M, Lam PC, Pinon DI, Orry A, Sexton PM, Abagyan R, Miller LJ.J Biol Chem. 2010201020100828
Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists.Katritch V, Jaakola VP, Lane JR, Lin J, Ijzerman AP, Yeager M, Kufareva I, Stevens RC, Abagyan R.J Med Chem. 2010201020095623
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex.Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R.Proteins. 2010201020063437GPCR Modeling Assessment
Recipes for the selection of experimental protein conformations for virtual screening.Rueda M, Bottegoni G, Abagyan R.J Chem Inf Model. 2010201020000587Induced Fit Docking
A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway.Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, Che CM.Cancer Res. 2010201019996284
Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold.Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, Salomon A, Williams C, Seaman MS, Abagyan R, Cardozo T, Gorny MK, Wang S, Lu S, Pinter A, Zolla-Pazner S.Virology. 2010201020663531
Conserved structural elements in the V3 crown of HIV-1 gp120.Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong XP.Nat Struct Mol Biol. 2010201020622876
Structural determinants of PERK inhibitor potency and selectivity.Wang H, Blais J, Ron D, Cardozo T.Chem Biol Drug Des. 2010201021070610Specific inhibitors identified by ICM-VLS.
Identification of new classes of ricin toxin inhibitors by virtual screening.Bai Y, Watt B, Wahome PG, Mantis NJ, Robertus JD.Toxicon. 2010201020493201
Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10.Endo S, Matsunaga T, Kuwata K, Zhao HT, El-Kabbani O, Kitade Y, Hara A.Bioorg Med Chem. 2010201020304656Discovery of several chomene-3carboxamide derivatives as potent competitive inhibitors.
Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression.Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM.Chemistry. 2009200919876976
SGC--structural biology and human health: a new approach to publishing structural biology results.Lee WH, Atienza-Herrero J, Abagyan R, Marsden BD.PLoS One. 2009200919847312ActiveICM
A new method for publishing three-dimensional content.Raush E, Totrov M, Marsden BD, Abagyan R.PLoS One. 2009200919841676ActiveICM
The flexible pocketome engine for structural chemogenomics.Abagyan R, Kufareva I.Methods Mol Biol. 2009200919727619
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands.Bisson WH, Koch DC, O'Donnell EF, Khalil SM, Kerkvliet NI, Tanguay RL, Abagyan R, Kolluri SK.J Med Chem. 2009200919719119Discovery of new class of AhR inhibitors.
FRODOCK: a new approach for fast rotational protein-protein docking.Garzon JI, Lop??z-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P.Bioinformatics. 2009200919620099
Homology modeling of GPCRs.Simms J, Hall NE, Lam PH, Miller LJ, Christopoulos A, Abagyan R, Sexton PM.Methods Mol Biol. 2009200919513644
Elucidation of the molecular basis of cholecystokinin Peptide docking to its receptor using site-specific intrinsic photoaffinity labeling and molecular modeling.Dong M, Lam PC, Pinon DI, Abagyan R, Miller LJ.Biochemistry. 2009200919441839
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.Rueda M, Bottegoni G, Abagyan R.J Chem Inf Model. 2009200919434904Induced Fit Docking
Functional importance of a structurally distinct homodimeric complex of the family B G protein-coupled secretin receptor.Gao F, Harikumar KG, Dong M, Lam PC, Sexton PM, Christopoulos A, Bordner A, Abagyan R, Miller LJ.Mol Pharmacol. 2009200919429716
Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes.Katritch V, Reynolds KA, Cherezov V, Hanson MA, Roth CB, Yeager M, Abagyan R.J Mol Recognit. 2009200919353579
Structure of the disordered C terminus of Rab7 GTPase induced by binding to the Rab geranylgeranyl transferase catalytic complex reveals the mechanism of Rab prenylation.Wu YW, Goody RS, Abagyan R, Alexandrov K.J Biol Chem. 2009200919240028
Structure-based approaches to antibiotic drug discovery.Nicola G, Abagyan R.Curr Protoc Microbiol. 2009200919235149
Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators.Reynolds KA, Katritch V, Abagyan R.J Comput Aided Mol Des. 2009200919148767
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.Bottegoni G, Kufareva I, Totrov M, Abagyan R.J Med Chem. 2009200919090659Induced Fit Docking
Computer applications for prediction of protein-protein interactions and rational drug design.Grosdidier S, Totrov M, Fern?­ndez-Recio J.Adv Appl Bioinform Chem. 2009200921918619
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.Bottegoni G, Kufareva I, Totrov M, Abagyan R.J Med Chem. 2009200919090659Induced Fit Docking
A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase.An J, Lee DC, Law AH, Yang CL, Poon LL, Lau AS, Jones SJ.J Med Chem. 2009200919419201Used MolSoft?s ICMPocketFinder to identify a new pocket conformation. Used ICM-VLS to identify a ligand with different binding pose and interactions than oseltamivir and zanamivir.
In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation.Wu S, Bottini M, Rickert RC, Mustelin T, Tautz L.ChemMedChem. 2009200919177473Sub and low micormolar inhibitors discovered using ICM-VLS.
Discovery of potent thermolysin inhibitors using structure based virtual screening and binding assays.Khan MT, Fuskev?g OM, Sylte I.J Med Chem. 2009200919072688NCI compound library screened and 12 inibitors discovered.
Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.Cross, J. B. et al.J. Chem. Inf. Model. 49, 1455.1474 (2009)200919476350VLS evaluation
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.Michino, M. et al.Nat. Rev. Drug Discov. 8, 455.463 (2009)2009 19461661GPCR docking and screening evaluation
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states.Kufareva I, Abagyan R.J Med Chem. 2008200819053777Kinase Modeling Method
Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations.Bisson WH, Abagyan R, Cavasotto CN.J Mol Graph Model. 2008200818805032
Damped-dynamics flexible fitting.Kovacs JA, Yeager M, Abagyan R.Biophys J. 2008200818586844
Spatial approximation between secretin residue five and the third extracellular loop of its receptor provides new insight into the molecular basis of natural agonist binding.Dong M, Lam PC, Pinon DI, Sexton PM, Abagyan R, Miller LJ.Mol Pharmacol. 2008200818467541
Discovery of a drug-like G-quadruplex binding ligand by high-throughput docking.Ma DL, Lai TS, Chan FY, Chung WH, Abagyan R, Leung YC, Wong KY.ChemMedChem. 2008200818383062
New method for the assessment of all drug-like pockets across a structural genome.Nicola G, Smith CA, Abagyan R.J Comput Biol. 2008200818333758
Flexible ligand docking to multiple receptor conformations: a practical alternative.Totrov M, Abagyan R.Curr Opin Struct Biol. 2008200818302984Induced Fit Docking Review
Optimization of high throughput virtual screening by combining shape-matching and docking methods.Lee HS, Choi J, Kufareva I, Abagyan R, Filikov A, Yang Y, Yoon S.J Chem Inf Model. 2008200818302357
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).Bottegoni G, Kufareva I, Totrov M, Abagyan R.J Comput Aided Mol Des. 2008200818273556Induced Fit Docking
Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin.Medina M, Abagyan R, G??mez-Moreno C, Fernandez-Recio J.Proteins. 2008200818260112
Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening.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.J Med Chem. 2008200818198821First demonstration that GPCR models can be used for antagonist discovery by virtual screening.
Towards a species-selective acetylcholinesterase inhibitor to control the mosquito vector of malaria, Anopheles gambiae.Carlier PR, Anderson TD, Wong DM, Hsu DC, Hartsel J, Ma M, Wong EA, Choudhury R, Lam PC, Totrov MM, Bloomquist JR.Chem Biol Interact. 2008200818554580
Atomic property fields: generalized 3D pharmacophoric potential for automated ligand superposition, pharmacophore elucidation and 3D QSAR.Totrov M.Chem Biol Drug Des. 2008200818069986Atomic Property Fields
3-Hydroxyanthranilic acid inhibits PDK1 activation and suppresses experimental asthma by inducing T cell apoptosis.Hayashi T, Mo JH, Gong X, Rossetto C, Jang A, Beck L, Elliott GI, Kufareva I, Abagyan R, Broide DH, Lee J, Raz E.Proc Natl Acad Sci U S A. 2007200718003900
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.Katritch V, Byrd CM, Tseitin V, Dai D, Raush E, Totrov M, Abagyan R, Jordan R, Hruby DE.J Comput Aided Mol Des. 2007200717960327230,000 available ketone and aldehyde compounds were screened. Out of 456 predicted ligands, 97 inhibitors of I7L proteinase activity were confirmed in biochemical assays.
De novo discovery of serotonin N-acetyltransferase inhibitors.Szewczuk LM, Saldanha SA, Ganguly S, Bowers EM, Javoroncov M, Karanam B, Culhane JC, Holbert MA, Klein DC, Abagyan R, Cole PA.J Med Chem. 20072007179246131.2 million compounds were screened and 241 compounds tested resulting in the discovery of a new class of inhibitors.
Small molecules block the polymerization of Z alpha1-antitrypsin and increase the clearance of intracellular aggregates.Mallya M, Phillips RL, Saldanha SA, Gooptu B, Brown SC, Termine DJ, Shirvani AM, Wu Y, Sifers RN, Abagyan R, Lomas DA.J Med Chem. 2007200717918823ICM-VLS was performed on 1.2 million small molecules and 6 antagonists were identified which were further optimized using ICM tools.
Three-dimensional structure of the EphB2 receptor in complex with an antagonistic peptide reveals a novel mode of inhibition.Chrencik JE, Brooun A, Recht MI, Nicola G, Davis LK, Abagyan R, Widmer H, Pasquale EB, Kuhn P.J Biol Chem. 2007200717897949
Fluorescence resonance energy transfer analysis of secretin docking to its receptor: mapping distances between residues distributed throughout the ligand pharmacophore and distinct receptor residues.Harikumar KG, Lam PC, Dong M, Sexton PM, Abagyan R, Miller LJ.J Biol Chem. 2007200717827151
Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs.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.Proc Natl Acad Sci U S A. 2007200717606915Screening to multiple receptor conformations of the androgen receptor led to the identification of an antagonist.
Sirtuin 2 inhibitors rescue alpha-synuclein-mediated toxicity in models of Parkinson's disease.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.Science. 2007200717588900
Molecular modeling and mutagenesis of gap junction channels.Kovacs JA, Baker KA, Altenberg GA, Abagyan R, Yeager M.Prog Biophys Mol Biol. 2007200717524457
Discovery of novel inhibitors targeting enoyl-acyl carrier protein reductase in Plasmodium falciparum by structure-based virtual screening.Nicola G, Smith CA, Lucumi E, Kuo MR, Karagyozov L, Fidock DA, Sacchettini JC, Abagyan R.Biochem Biophys Res Commun. 2007200717509532ChemBridge database was screened. 169 compounds were tested experimentally and 16 compounds had activity.
Self-assembling cannabinomimetics: supramolecular structures of N-alkyl amides.Raduner S, Bisson W, Abagyan R, Altmann KH, Gertsch J.J Nat Prod. 2007200717497806
Computational prediction of atomic structures of helical membrane proteins aided by EM maps.Kovacs JA, Yeager M, Abagyan R.Biophys J. 2007200717496035
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.Dong M, Lam PC, Gao F, Hosohata K, Pinon DI, Sexton PM, Abagyan R, Miller LJ.Mol Pharmacol. 2007200717475809
Role of lysine187 within the second extracellular loop of the type A cholecystokinin receptor in agonist-induced activation. Use of complementary charge-reversal mutagenesis to define a functionally important interdomain interaction.Dong M, Ding XQ, Thomas SE, Gao F, Lam PC, Abagyan R, Miller LJ.Biochemistry. 2007200717381074
PIER: protein interface recognition for structural proteomics.Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R.Proteins. 2007200717299750
DFprot: a webtool for predicting local chain deformability.Garz??n JI, Kovacs J, Abagyan R, Chac??n P.Bioinformatics. 2007200717277334
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage.Garz??n JI, Kovacs J, Abagyan R, Chac??n P.Bioinformatics. 2007200717150992
Functional conservation of Rel binding sites in drosophilid genomes.Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA.Genome Res. 2007200717785540
Waltzing transporters and 'the dance macabre' between humans and bacteria.Lomovskaya O, Zgurskaya HI, Totrov M, Watkins WJ.Nat Rev Drug Discov. 2007200717159924
In silico prediction of SARS protease inhibitors by virtual high throughput screening.Plewczynski D, Hoffmann M, von Grotthuss M, Ginalski K, Rychewski L.Chem Biol Drug Des. 2007200717461975
Assay principle for modulators of protein-protein interactions and its application to non-ATP-competitive ligands targeting protein kinase A.Saldanha SA, Kaler G, Cottam HB, Abagyan R, Taylor SS.Anal Chem. 2006200617165815
The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure.Malinina L, Malakhova ML, Kanack AT, Lu M, Abagyan R, Brown RE, Patel DJ.PLoS Biol. 2006200617105344
On evaluating molecular-docking methods for pose prediction and enrichment factors.Chen, H., Lyne, P. D., Giordanetto, F., Lovell, T. & Li, J.J. Chem. Inf. Model. 46, 401.415 (2006)200616426074Independent VLS evaluation.
Weighted quality estimates in machine learning.Budagyan L, Abagyan R.Bioinformatics. 2006200616935929
Discovery of bioactive small-molecule inhibitor of poly adp-ribose polymerase: implications for energy-deficient cells.Altmann SM, Muryshev A, Fossale E, Maxwell MM, Norflus FN, Fox J, Hersch SM, Young AB, MacDonald ME, Abagyan R, Kazantsev AG.Chem Biol. 2006200616873024
Defining the CD59-C9 binding interaction.Huang Y, Qiao F, Abagyan R, Hazard S, Tomlinson S.J Biol Chem. 2006200616844690
Structure-based development of target-specific compound libraries.Orry AJ, Abagyan RA, Cavasotto CN.Drug Discov Today. 2006200616580603
Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes.Bordner AJ, Abagyan R.Proteins. 2006200616470819
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G.Anal Chem. 2006200616448051
In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells.Cavasotto CN, Ortiz MA, Abagyan RA, Piedrafita FJ.Bioorg Med Chem Lett. 2006200616413185300K compounds were screened > 7 micromolar hits identified.
Disseminating structural genomics data to the public: from a data dump to an animated story.Abagyan R, Lee WH, Raush E, Budagyan L, Totrov M, Sundstrom M, Marsden BD.Trends Biochem Sci. 2006200616406633ActiveICM
METLIN: a metabolite mass spectral database.Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G.Ther Drug Monit. 2005200516404815
Druggability of SCF ubiquitin ligase-protein interfaces.Cardozo T, Abagyan R.Methods Enzymol. 2005200516338386
Small molecule inhibitors of dynamin I GTPase activity: development of dimeric tyrphostins.Hill T, Odell LR, Edwards JK, Graham ME, McGeachie AB, Rusak J, Quan A, Abagyan R, Scott JL, Robinson PJ, McCluskey A.J Med Chem. 2005200516302817
Surrogate data--a secure way to share corporate data.Tetko IV, Abagyan R, Oprea TI.J Comput Aided Mol Des. 2005200516267691
Insights into the human CD59 complement binding interface toward engineering new therapeutics.Huang Y, Smith CA, Song H, Morgan BP, Abagyan R, Tomlinson S.J Biol Chem. 2005200516079145
Representing receptor flexibility in ligand docking through relevant normal modes.Cavasotto CN, Kovacs JA, Abagyan RA.J Am Chem Soc. 2005200515984891
Efficient synthetic inhibitors of anthrax lethal factor.Forino M, Johnson S, Wong TY, Rozanov DV, Savinov AY, Li W, Fattorusso R, Becattini B, Orry AJ, Jung D, Abagyan RA, Smith JW, Alibek K, Liddington RC, Strongin AY, Pellecchia M.Proc Natl Acad Sci U S A. 2005200515983377
Improving CAPRI predictions: optimized desolvation for rigid-body docking.Fern??ndez-Recio J, Abagyan R, Totrov M.Proteins. 2005200515981266
Statistical analysis and prediction of protein-protein interfaces.Bordner AJ, Abagyan R.Proteins. 2005200515906321
Pocketome via comprehensive identification and classification of ligand binding envelopes.An J, Totrov M, Abagyan R.Mol Cell Proteomics. 2005200515757999ICMPocketFinder
REVCOM: a robust Bayesian method for evolutionary rate estimation.Bordner AJ, Abagyan R.Bioinformatics. 2005200515749694
Optimal docking area: a new method for predicting protein-protein interaction sites.Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R.Proteins. 2005200515495260Optimal Docking Area
Vacuuming the periplasm.Lomovskaya O, Totrov M.J Bacteriol. 2005200515743933
Comprehensive identification of druggable" protein ligand binding sites."An J, Totrov M, Abagyan R.Genome Inform. 2004200415706489ICMPocketFinder
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations.Bordner AJ, Abagyan RA.Proteins. 2004200415340927
Determinants of retinoid X receptor transcriptional antagonism.Cavasotto CN, Liu G, James SY, Hobbs PD, Peterson VJ, Bhattacharya AA, Kolluri SK, Zhang XK, Leid M, Abagyan R, Liddington RC, Dawson MI.J Med Chem. 2004200415317450
Predictions of protein flexibility: first-order measures.Kovacs JA, Chac??n P, Abagyan R.Proteins. 2004200415281119
Long chain amines and long chain ammonium salts as novel inhibitors of dynamin GTPase activity.Hill TA, Odell LR, Quan A, Abagyan R, Ferguson G, Robinson PJ, McCluskey A.Bioorg Med Chem Lett. 2004200415149689
SAD--a normalized structural alignment database: improving sequence-structure alignments.Marsden B, Abagyan R.Bioinformatics. 2004200415087320
Protein flexibility in ligand docking and virtual screening to protein kinases.Cavasotto CN, Abagyan RA.J Mol Biol. 2004200415001363
Identification of protein-protein interaction sites from docking energy landscapes.Fern??ndez-Recio J, Totrov M, Abagyan R.J Mol Biol. 2004200414687579
A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening.Howard MH, Cenizal T, Gutteridge S, Hanna WS, Tao Y, Totrov M, Wittenbach VA, Zheng YJ.J Med Chem. 2004200415615515
Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking.Totrov M.J Comput Chem. 2004200414735578
Comparative study of several algorithms for flexible ligand docking.Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd.J Comput Aided Mol Des. 2003200315072435 VLS Evaluation
Algorithms for high-density oligonucleotide array.Zhou Y, Abagyan R.Curr Opin Drug Discov Devel. 2003200312833666
Nuclear hormone receptor targeted virtual screening.Schapira M, Abagyan R, Totrov M.J Med Chem. 2003200312825943
ICM-DISCO docking by global energy optimization with fully flexible side-chains.Fern??ndez-Recio J, Totrov M, Abagyan R.Proteins. 2003200312784376
Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking.Schapira M, Raaka BM, Das S, Fan L, Totrov M, Zhou Z, Wilson SR, Abagyan R, Samuels HH.Proc Natl Acad Sci U S A. 2003200312777627250K compounds were screened, 75 were tested experimentally and 14 antagonists were discovered.
Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.Cavasotto CN, Orry AJ, Abagyan RA.Proteins. 2003200312696053
The transthyretin-related protein family.Eneqvist T, Lundberg E, Nilsson L, Abagyan R, Sauer-Eriksson AE.Eur J Biochem. 2003200312542701
ICFF: a new method to incorporate implicit flexibility into an internal coordinate force field.Katritch V, Totrov M, Abagyan R.J Comput Chem. 2003200312497604
Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum.Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA.Science. 2002200212364807
Computational structural proteomics.Brive L, Abagyan R.Ernst Schering Res Found Workshop. 2002200212061000
Screened charge electrostatic model in protein-protein docking simulations.Fernandez-Recio J, Totrov M, Abagyan R.Pac Symp Biocomput. 2002200211928507
Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine.Schapira M, Abagyan R, Totrov M.BMC Struct Biol. 2002200211860617
Match-only integral distribution (MOID) algorithm for high-density oligonucleotide array analysis.Zhou Y, Abagyan R.BMC Bioinformatics. 2002200211835687
Soft protein-protein docking in internal coordinates.Fern??ndez-Recio J, Totrov M, Abagyan R.Protein Sci. 2002200211790838
High-throughput docking for lead generation.Abagyan R, Totrov M.Curr Opin Chem Biol. 2001200111470599
Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.Totrov M, Abagyan R.Biopolymers. 2001200111455546Electrostatics
In silico discovery of novel retinoic acid receptor agonist structures.Schapira M, Raaka BM, Samuels HH, Abagyan R.BMC Struct Biol. 2001200111405897
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov VV, Peter MG, Wierenga RK.Proteins. 2001200111151009
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR.Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL.J Comput Aided Mol Des. 2000200010921774High enrichment factor and 7 new inhibitors identified.
Antibodies against thrombospondin-related anonymous protein do not inhibit Plasmodium sporozoite infectivity in vivo.Gantt S, Persson C, Rose K, Birkett AJ, Abagyan R, Nussenzweig V.Infect Immun. 2000200010816526
Genetic linkage mapping of zebrafish genes and ESTs.Kelly PD, Chu F, Woods IG, Ngo-Hazelett P, Cardozo T, Huang H, Kimm F, Liao L, Yan YL, Zhou Y, Johnson SL, Abagyan R, Schier AF, Postlethwait JH, Talbot WS.Genome Res. 2000200010779498
Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition.Jin E, Katritch V, Olson WK, Kharatisvili M, Abagyan R, Pilch DS.J Mol Biol. 2000200010756107
Expression of the adenovirus receptor and its interaction with the fiber knob.Tomko RP, Johansson CB, Totrov M, Abagyan R, Fris??n J, Philipson L.Exp Cell Res. 2000200010666333
Rational discovery of novel nuclear hormone receptor antagonists.Schapira M, Raaka BM, Samuels HH, Abagyan R.Proc Natl Acad Sci U S A. 2000200010655475
Estimating local backbone structural deviation in homology models.Cardozo T, Batalov S, Abagyan R.Comput Chem. 2000200010642877
Expression of the adenovirus receptor and its interaction with the fiber knob.Tomko RP, Johansson CB, Totrov M, Abagyan R, Fris??n J, Philipson L.Exp Cell Res. 2000200010666333
NRIF3 is a novel coactivator mediating functional specificity of nuclear hormone receptors.Li D, Desai-Yajnik V, Lo E, Schapira M, Abagyan R, Samuels HH.Mol Cell Biol. 1999199910490654
Derivation of Sensitive Discrimination Potential for Virtual Ligand ScreeningTotrov, M.M., and Abagyan R.A.Proceedings of the Third Annual Intl. Conf. on Comp. Mol. Bio. 312-320 19991999Description of ICM VLS Scoring
Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics.Stigler RD, Hoffmann B, Abagyan R, Schneider-Mergener J.Structure. 1999199910404595
Prediction of the binding energy for small molecules, peptides and proteins.Schapira M, Totrov M, Abagyan R.J Mol Recognit. 1999199910398408Binding Energy
A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences.Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WS.Genome Res. 1999199910207156
Identification of the individual residues that determine human CD59 species selective activity.Zhang HF, Yu J, Chen S, Morgan BP, Abagyan R, Tomlinson S.J Biol Chem. 1999199910196177
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains.Zhou Y, Abagyan R.Fold Des. 199819989889165
Novel anchorage of GluR2/3 to the postsynaptic density by the AMPA receptor-binding protein ABP.Srivastava S, Osten P, Vilim FS, Khatri L, Inman G, States B, Daly C, DeSouza S, Abagyan R, Valtschanoff JG, Weinberg RJ, Ziff EB.Neuron. 199819989768844
Identification and analysis of PH domain-containing targets of phosphatidylinositol 3-kinase using a novel in vivo assay in yeast.Isakoff SJ, Cardozo T, Andreev J, Li Z, Ferguson KM, Abagyan R, Lemmon MA, Aronheim A, Skolnik EY.EMBO J. 199819989736615
Energy strain in three-dimensional protein structures.Maiorov V, Abagyan R.Fold Des. 199819989710569Protein Health
TNF-alpha convertase enzyme from human arthritis-affected cartilage: isolation of cDNA by differential display, expression of the active enzyme, and regulation of TNF-alpha.Patel IR, Attur MG, Patel RN, Stuchin SA, Abagyan RA, Abramson SB, Amin AR.J Immunol. 199819989574564
The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK.J Mol Biol. 199719979402066
Do aligned sequences share the same fold?Abagyan RA, Batalov S.J Mol Biol. 199719979367768
Evaluating the energetics of empty cavities and internal mutations in proteins.Rashin AA, Rashin BH, Rashin A, Abagyan R.Protein Sci. 199719979336837
Mapping the regions of the complement inhibitor CD59 responsible for its species selective activity.Yu J, Dong S, Rushmere NK, Morgan BP, Abagyan R, Tomlinson S.Biochemistry. 199719979235986
TSG101 may be the prototype of a class of dominant negative ubiquitin regulators.Koonin EV, Abagyan RA.Nat Genet. 199719979241264
Contact area difference (CAD): a robust measure to evaluate accuracy of protein models.Abagyan RA, Totrov MM.J Mol Biol. 199719979171291
A new method for modeling large-scale rearrangements of protein domains.Maiorov V, Abagyan R.Proteins. 199719979094743
Mapping the active site of CD59.Yu J, Abagyan R, Dong S, Gilbert A, Nussenzweig V, Tomlinson S.J Exp Med. 199719979034152
Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.Thanki N, Zeelen JP, Mathieu M, Jaenicke R, Abagyan RA, Wierenga RK, Schliebs W.Protein Eng. 199719979089815
Flexible protein-ligand docking by global energy optimization in internal coordinates.Totrov M, Abagyan R.Proteins. 199719979485515Docking
Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search.Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y.Proteins. 199719979485492Homology Modeling
Long pentraxins: an emerging group of proteins with diverse functions.Goodman AR, Cardozo T, Abagyan R, Altmeyer A, Wisniewski HG, Vilcek J.Cytokine Growth Factor Rev. 199619968899296
The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data.Chalikian TV, Totrov M, Abagyan R, Breslauer KJ.J Mol Biol. 199619968759322
Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase.Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN.Nat Struct Biol. 199619968605624
The contour-buildup algorithm to calculate the analytical molecular surface.Totrov M, Abagyan R.J Struct Biol. 199619968742735
Homology modeling by the ICM method.Cardozo T, Totrov M, Abagyan R.Proteins. 199519958710833Homology Modeling
Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8.Borchert TV, Kishan KV, Zeelen JP, Schliebs W, Thanki N, Abagyan R, Jaenicke R, Wierenga RK.Structure. 199519958591044
Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability.Houbrechts A, Moreau B, Abagyan R, Mainfroid V, Pr??aux G, Lamproye A, Poncin A, Goormaghtigh E, Ruysschaert JM, Martial JA, et al.Protein Eng. 199519957479687
The protein folding problem: finding a few minimums in a near infinite space.Argos P, Abagyan R.Comput Chem. 199419947952893
Recognition of distantly related proteins through energy calculations.Abagyan R, Frishman D, Argos P.Proteins. 199419948090707
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy.Totrov M, Abagyan R.Nat Struct Biol. 199419947656055
Design, creation, and characterization of a stable, monomeric triosephosphate isomerase.Borchert TV, Abagyan R, Jaenicke R, Wierenga RK.Proc Natl Acad Sci U S A. 199419948108439
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.Abagyan R, Totrov M.J Mol Biol. 199419948289329ICM Global Optimization Method
ICM - a new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation.Abagyan R, Totrov M. , Kuznetsov DJ Comp Chem. 19941994ICM Method Description
A technique for identifying atoms from a screen image.Kuznetsov DA, Abagyan RA.J Mol Graph. 199319938136327
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.Borchert TV, Abagyan R, Kishan KV, Zeelen JP, Wierenga RK.Structure. 1993199316100954
Towards protein folding by global energy optimization.Abagyan RA.FEBS Lett. 199319938513887
A method to configure protein side-chains from the main-chain trace in homology modelling.Eisenmenger F, Argos P, Abagyan R.J Mol Biol. 199319938515455
Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins.Gibson TJ, Thompson JD, Abagyan RA.Protein Eng. 199319938433970
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.Abagyan R, Argos P.J Mol Biol. 199219921593634
Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model.Abagyan RA, Mironov VN, Chernov BK, Chuprina VP, Ulyanov AV.Nucleic Acids Res. 199019902315048
Sequence dependent modulating effect of camptothecin on the DNA-cleaving activity of the calf thymus type I topoisomerase.Gromova II, Buchman VL, Abagyan RA, Ulyanov AV, Bronstein IB.Nucleic Acids Res. 199019902155407
Structure of the hydration shells of oligo(dA-dT).oligo(dA-dT) and oligo(dA).oligo(dT) tracts in B-type conformation on the basis of Monte Carlo calculations.Eisenhaber F, Tumanyan VG, Abagyan RA.Biopolymers. 199019902265229
An automatic search for similar spatial arrangements of alpha-helices and beta-strands in globular proteins.Abagyan RA, Maiorov VN.J Biomol Struct Dyn. 198919892818856
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles.Abagyan RA, Mazur AK.J Biomol Struct Dyn. 198919892619943
New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures.Mazur AK, Abagyan RA.J Biomol Struct Dyn. 198919892619942
Structural basis of stable bending in DNA containing An tracts. Different types of bending.Chuprina VP, Abagyan RA.J Biomol Struct Dyn. 198819883271514
A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structures.Abagyan RA, Maiorov VN.J Biomol Struct Dyn. 198819883271511
Anomalous properties of adenine.thymine tracts.Chuprina VP, Abagyan RA.Nature. 198819883347251
[Block improvement of the genetic text as a factor of acceleration of biological evolution].Ivanitski?? GR, Esipova NG, Abagyan RA, Shnol' SE.Biofizika. 198519854027270
[Two types of tripeptide conformation in collagen. Calculation of the structure of (Gly-Pro-Ser)n and (Gly-Val-Hyp)n polytripeptides].Abagyan RA, Tumanian VG, Esipova NG.Bioorg Khim. 198419846548632
[Arrangement of molecular packing of collagen in fibrils].Abagyan RA.Biofizika. 198319836871272
[Diffraction from the alternating helix].Abagyan RA.Biofizika. 198319836871260
[Diffraction effects on x-rays of the oligotripeptide (Gly-Pro-Pro)10, isomorphic to collagen].Rogulenkova VN, Abagyan RA, Tumanian VG, Esipova NG.Biofizika. 198119817284464

Site Map | Request a Trial | What's New | Knowledge Base | Videos

© 2024 All Rights Reserved MolSoft LLC Terms of Use | Privacy Policy