CMM Publications
To modify an entry click on the corresponding icon
To add new publication click submit new
- In Silico Approaches to Structure and Function of Cell Components and Their Assemblies; in Comprehensive Biophysics; S. A. Hassan and E. L. Mehler, Vol. 9, pp 190-228, Academic Press (2011) [Full Article]
- Microscopic Mechanism of Nanocrystal Formation from Solution by Cluster Aggregation and Coalescence S A Hassan; J. Chem. Phys. 134, 114508 (2011)
[Abstract] [Full Article] - "Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions" S. A. Hassan; J. Phys. Chem. B 112, 10573 (2008)
[Abstract] [Full Article] - J. Pavlicek, S. L. Coon, S. Ganguly, J. L. Weller, S. A. Hassan, D. L. Sackett, and D. C. Klein "Evidence that Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase" J. Biol. Chem. 283, 14552 (2008)
[Abstract] [Full Article] - S. A. Hassan Morphology of Ion Clusters in Aqueous Electrolytes; Phy. Rev. E 77, 031501 (2008)
[Abstract] [Full Article] - Hiebel AC, Lee YS, Bilsky E, Giuvelis D, Deschamps JR, Parrish DA, Aceto MD, May EL, Harris LS, Coop A, Dersch CM, Partilla JS, Rothman RB, Cheng, K, Jacobson AE, Rice KC "Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent m-Agonist d-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series" J. Med. Chem. 2007, 50, 3765-3776
[Abstract] - S. A. Hassan, "Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution", J. Phys. Chem. B 111 , 227 (2007)
[Abstract] [Full Article] - Z.Xiang, "Advances in homology protein structure modeling", Curr. Prot. Pept. Sci. 7:217, (2006)
[Abstract] [PubMed] - SA Hassan, G Hummer, and YS Lee "Effects of Electric Fields on Proton Transport through Water Chains" J. Chem. Phys. 124, 204510 (2006)
[Abstract] [Full Article] - Li X, Hassan SA, Mehler EL "Long Dynamics Simulations of Proteins using Atomistic Forcefields and Continuum Representation of Solvent Effects: Calculation of Structural and Dynamics Properties" Proteins 60:464-484 (2006) Full Article
- Sergio A. Hassan "Amino Acid Side Chain Interactions in the Presence of Salts" J. Phys. Chem. B 109:21989 (2005) Full Article
- Hassan SA, Mehler EL "From Quantum Chemistry and the Classical Theory of Polar Liquids to Continuum Approximations in Molecular Mechanics Calculations" Int. J. Quant. Chem. 102:986-1001 (2005) Full Article
- Hassan SA, Gracia L, Vasudevan G, Steinbach PJ "Computer Simulation of Protein-Ligand Interactions: Challenges and Applications." Protein-Ligand Interactions: Methods and Applications Nienhaus, G. Ulrich, editor. Humana Press. pp. 451-492 (2005)
- Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H"Mechanistic Insights from a Refined Three-dimensional Model of Integrin aphaIIb-beta3" J. Biol. Chem. 279:24624 (2004)
[PubMed] - Hassan SA "Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium" J. Phys. Chem. B 108:19501 (2004) Full Article
- Lee YS and Krauss M
"Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase." J. Phys. Chem. B. 108: 4508-4515 - Lee YS and Krauss M
"Dynamics of Proton Transfer in Bacteriorhodopsin." J. Am. Chem. Soc. 126: 2225-2230
[PubMed] - Lee YS, Monica GM and Necker L
"Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans-Cis Isomerization of Geldanamycin." Chemistry and Biology 11: 991-8
[PubMed] - J. Tang, S. Stern-Nezer, P.-C. Liu, L. Matyakhina, M. Riordan, N.L.C. Luban, P.J. Steinbach & S.G. Kaler
"Mutation in the Leucine-rich Repeat C-flanking Region of Platelet Glycoprotein Ib-beta Impairs Assembly of von Willebrand Factor Receptor." Thromb. Haemost. 92: 75-88
[PubMed] - P.J. Steinbach
"Exploring Peptide Energy Landscapes: A Test of Force Fields and Implicit Solvent Models." Proteins Struct. Funct. Bioinform. 57: 665-677
[PubMed] - Lee, YS, Hodoscek M., Kador PF and Sugiyama K
"Hydrogen bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay." Chem-Biol Interact. 143: 307-316
[PubMed] - Woodcock HL, Hodoscek M, Sherwood P, Lee YS, Schafer III HF and Brooks BR
"Exploring the QM/MM Replica Method: A pathway optimization of the chorismate to prephenate Claisen Rearrangement Catalyzed by Chorismate Mutase." Theor. Chem. Acc. 109: 140-148 - Lee YS, Worthington SE, Krauss M and Brooks BR
"Reaction Mechansim of Chorismate Mutase Studied by the Comibined Potentials of Quantum Mechanics and Molecular Mechanics." J. Phys. Chem. B 106: 12059-12065 - P.J. Steinbach, R. Ionescu, & C.R. Matthews
"Analysis of Kinetics using a Hybrid Maximum-Entropy / Nonlinear-Least-Squares Method: Application to Protein Folding." Biophys. J. 82: 2244-2255
[PubMed] - P.J. Steinbach
"Inferring Lifetime Distributions from Kinetics by Maximizing Entropy Using a Bootstrapped Model." J. Chem. Inf. Comput. Sci. 42: 1476-1478
[PubMed] - Dhanvantari S, Arnaoutova I, Snell CR, Steinbach PJ, Hammond K, Caputo GA, London E, Loh YP
"Carboxypeptidase E, a prohormone sorting receptor, is anchored to secretory granules via a C-terminal transmembrane insertion." Biochemistry 41: 52-60
[PubMed] - R. Chu, J. Takei, J.R. Knowlton, M. Andrykovitch, W. Pei, A.V. Kajava, P.J. Steinbach, X. Ji & Y. Bai
"Redesign of a Four-helix Bundle Protein by Phage Display Coupled with Proteolysis and Structural Characterization by NMR and X-ray Crystallography." J. Mol. Biol. 323: 253-62
[PubMed] - L.J. Lapidus, P.J. Steinbach, W.A. Eaton, A. Szabo & J. Hofrichter
"Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides." J. Phys. Chem. B 106: 11628-11640 - G. Reyes-Cruz, J. Hu, P.K. Goldsmith, P.J. Steinbach, & A.M. Spiegel
"Human Ca Receptor Extracellular Domain: Analysis of Function of Lobe I Loop Deletion Mutants." J. Biol. Chem. 276: 32145-32151
[PubMed] - J. Piatigorsky, B. Norman, L.J. Dishaw, L. Kos, J. Horwitz, P.J. Steinbach & Z. Kozmik
"J3-Crystallin of the Jellyfish Lens: Homology to Saposins." Proc. Natl. Acad. Sci. USA 98: 12362-12367 - S. Ganguly, P. Mummaneni, P.J. Steinbach, D.C. Klein & S.L.Coon
"Characterization of the Saccharomyces cerevisiae Homolog of the Melatonin Rhythm Enzyme Arylalkylamine N-acetyltransferase (AANAT, EC 2.3.1.87)." J. Biol. Chem. 276: 47239-47247
[PubMed] - Chamberlin ME, Ubagai T, Pao VY, Pearlstein RA, and Chou JY
"Structural requirements for catalysis and dimerization of human methionine adenosyltransferase I/III." Arch Biochem Biophys 373 (1): 56-62
[Abstract] [PubMed] - Sugiyama K, Chen Z, Lee YS and Kador PF
"Isolation of a Non-covalent Aldose Reductase-Nucleotide-Inhibitor Complex." Biochem. Pharmacol. 59: 329-336
[PubMed] - J.J. Balbach, J. Yang, D.P. Weliky, P.J. Steinbach, V. Turganov, J. Anglister & R. Tycko
"Probing Hydrogen Bonds in the Antibody-Bound HIV-1 gp120 V3 Loop by Solid State NMR REDOR Measurements." J. Biomol. NMR 16: 313-327
[PubMed] - J. Piatigorsky, Z. Kozmik, J. Horwitz, L. Ding, E. Carosa, W.G. Robison, Jr., P.J. Steinbach & E.R. Tamm
"Omega-Crystallin of the Scallop Lens: A Dimeric Aldehyde Dehydrogenase Class 1/2 Enzyme-Crystallin." J. Biol. Chem. 275: 41064-41073
[PubMed] - Rizzo P, Tinello C, Pearlstein RA, and Taniuchi H
"Antibody immunodiversity: A study on the marked specificity difference between two anti-yeast iso-1 cytochrome c monoclonal antibodies whose epitopes are closely related." J Protein Chem. 18 (5): 523-532
[Abstract] [PubMed] - Lee YS, Sugiyama K and Kador PF
"Rotamers of Tolrestat and Their Binding Mode to Aldose Reductase." Adv. Exp. Med. Biol. 463: 465-472
[PubMed] - D.P. Weliky, A.E. Bennett, A. Zvi, J. Anglister, P.J. Steinbach & R. Tycko
"Solid-State NMR Evidence for an Antibody-Dependent Conformation of the V3 Loop of HIV-1 gp120." Nature Struct. Biol. 6: 141-145
[PubMed] - P. Sharma, P.J. Steinbach, M. Sharma, N.D. Amin, J.J. Barchi, Jr. & H.C. Pant
"Identification of Substrate Binding Site of Cyclin-Dependent Kinase 5." J. Biol. Chem. 274: 9600-9606
[PubMed] - K. Ray, B.C. Hauschild, P.J. Steinbach, P.K. Goldsmith, O. Hauache & A.M. Spiegel
"Identification of the Cysteine Residues in the Amino-Terminal Extracellular Domain of the Human Ca Receptor Critical for Dimerization: Implications for Function of Monomeric Ca Receptor." J. Biol. Chem. 274: 27642-27650
[PubMed] - Lee YS, Chen Z and Kador PF
"Molecular Modeling Studies of the Binding Modes of Aldose Reductase Inhibitors at the Active Site of Human Aldose Reductase." Bioorg. Med. Chem. 6: 1811-1820
[PubMed] - Lee YS, Hodoscek M, Brooks B and Kador PF
"Catalytic Mechanism of Aldose Reductase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics." Biophys. Chem. 274: 27642-27650
[PubMed] - E. Leroy, R. Boyer, G. Auburger, B. Leube, G. Ulm, E. Mezey, G. Harta, M.J. Brownstein, S. Jonnalagada, T. Chernova, A. Dehejia, C. Lavedan, T. Gasser, P.J. Steinbach, K.D. Wilkinson & M.H Polymeropoulos
"The Ubiquitin Pathway in Parkinson's Disease." Nature 395: 451-452
[PubMed] - Lin ZL, Shenker A, and Pearlstein RA
"A model of the lutropin/choriogonadotropin receptor: Insights into the structural and functional effects of constitutively activating mutations." Protein Eng. 10 (5): 501-510
[Abstract] [PubMed] - P.J. Steinbach
"Two-Dimensional Distributions of Activation Enthalpy and Entropy from Kinetics by the Maximum Entropy Method." Biophys. J. 70: 1521-1528
[PubMed] - P.J. Steinbach & B.R. Brooks
"Hydrated Myoglobin's Anharmonic Fluctuations are Not Primarily Due to Dihedral Transitions." Proc. Natl. Acad. Sci. USA 93: 55-59 - Lee YS, Pearlstein R and Kador PF
"Molecular Modeling Studies of Aldose Reductase Inhibitors." J. Med. Chem. 37: 787-792
[PubMed] - P.J. Steinbach & B.R. Brooks
"New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation." J. Comp. Chem. 15: 667-683 - Y. Osawa, J.F. Darbyshire, P.J. Steinbach, & B.R. Brooks
"Metabolism-Based Transformation of Myoglobin to an Oxidase by BrCCl and Molecular Modeling of the Oxidase Form." J. Biol. Chem. 268: 2953-2959 - P.J. Steinbach & B.R. Brooks
"Protein Hydration Elucidated by Molecular Dynamics Simulation." Proc. Natl. Acad. Sci. USA 90: 9135-9139
[PubMed] - Hong SY, Kertesz M, Lee YS and Kim OK
"Geometrical and Electronic Structures of Benzimidazobenzophenanthroline-Type Ladder Polymer (BBL)." Macromolecules 25: 5424-5429 - Kindle JR, Bartoli FJ, Hoffman CA, Kim OK, Lee YS, Shirk JS and Kafafi ZH
"Nonlinear Optical Properties of Heteroaromatic Ladder Polymers, BBL and BBB at 1.064 um." Appl. Phys. Lett. 56: 712-717 - Lee YS, Kertesz M and Elsenbaumer RL
"The Importance of Energetics in the Design and Synthesis of Small Band Gap Conducting Polymer." Chem. Mater. 2: 526-530