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Abbreviation : ES
Long Form : enzyme-substrate
No. Year Title Co-occurring Abbreviation
2020 Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. QM/MM
2020 Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires. ATP, cAMP, MD, QM/MM
2020 The Soybean Lipoxygenase-Substrate Complex: Correlation between the Properties of Tunneling-Ready States and ENDOR-Detected Structures of Ground States. DAD, ENDOR, LA, SLO, TRS
2019 Steroidal fraction of Carissa carandas L. inhibits microbial hyaluronidase activity by mixed inhibition mechanism. HA, SF
2018 Catalytic Mechanism of Amyloid-beta Peptide Degradation by Insulin Degrading Enzyme: Insights from Quantum Mechanics and Molecular Mechanics Style Moller-Plesset Second Order Perturbation Theory Calculation. IDE, QM/MM
2018 Kinetics and stereochemistry of LinB-catalyzed delta-HBCD transformation: Comparison of invitro and in silico results. EP, HBCDs, HCH, MM, PBCDols, TBCDdiols
2018 Modeling the Transient Kinetics of the L1 Metallo-beta-Lactamase. EP, MbetaL, QM/MM, TD-DFT
2018 Partial purification and characterization of serine protease produced through fermentation of organic municipal solid wastes by Serratia marcescens A3 and Pseudomonas putida A2. Ea, MSW
2017 A receptor dependent-4D QSAR approach to predict the activity of mutated enzymes. RD-4D-QSAR
10  2017 Alzheimer's-Causing Mutations Shift Abeta Length by Destabilizing gamma-Secretase-Abetan Interactions. AD, APP, PSEN
11  2017 Set of Fe(II)-3-Hydroxyflavonolate Enzyme-Substrate Model Complexes of Atypically Coordinated Mononuclear Non-Heme Fe(II)-Dependent Quercetin 2,4-Dioxygenase. Fe-2,4-QD, LRH
12  2017 Simulating the slow to fast switch in cytochrome c oxidase catalysis by introducing a loop flip near the enzyme's cytochrome c (substrate) binding site. COX
13  2016 Capture of a third Mg⁺ is essential for catalyzing DNA synthesis. ---
14  2016 Enzyme Substrate Complex of the H200C Variant of Homoprotocatechuate 2,3-Dioxygenase: Mossbauer and Computational Studies. EFG, H200C, HPCD, ZFS
15  2016 Modeling the Complete Catalytic Cycle of Aspartoacylase. ASPA, EP, MD, QM/MM
16  2014 A series of Ni(II)-flavonolate complexes as structural and functional ES (enzyme-substrate) models of the Ni(II)-containing quercetin 2,3-dioxygenase. 2,3-QD
17  2014 Series of structural and functional models for the ES (enzyme-substrate) complex of the Co(II)-containing quercetin 2,3-dioxygenase. Co-2,3-QD
18  2013 Flavonolate complexes of M(II) (M = Mn, Fe, Co, Ni, Cu, and Zn). Structural and functional models for the ES (enzyme-substrate) complex of quercetin 2,3-dioxygenase. 2,3-QD
19  2013 Modifying the catalytic preference of tributyrin in Bacillus thermocatenulatus lipase through in-silico modeling of enzyme-substrate complex. MD, SMD
20  2013 On quantum mechanical--molecular mechanical (QM/MM) approaches to model hydrolysis of acetylcholine by acetylcholinesterase. QM/MM, TI
21  2013 Structure-based computational study of the hydrolysis of New Delhi metallo-beta-lactmase-1. NDM-1
22  2012 Active site intermediates in the reduction of O(2) by cytochrome oxidase, and their derivatives. ---
23  2012 In situ monitoring of a trace intermediate during DNA phosphorylation by T4 polynucleotide kinase for transient kinetic studies. QCM, T4 PNK
24  2011 Human butyrylcholinesterase-cocaine binding pathway and free energy profiles by molecular dynamics and potential of mean force simulations. BChE, bind, PMF
25  2011 Influence of water on the formation of O2-reactive divalent metal enolate complexes of relevance to acireductone dioxygenases. ---
26  2011 Mechanistic studies of the O2-dependent aliphatic carbon-carbon bond cleavage reaction of a nickel enolate complex. ARDs
27  2011 Prechemistry versus preorganization in DNA replication fidelity. PMF
28  2010 Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies. AChE, QM/MM
29  2009 FT-IR spectroscopic studies on the molecular mechanism for substrate specificity/activation of medium-chain acyl-CoA dehydrogenase. MCADs
30  2009 In vitro effect of ozagrel on mushroom tyrosinase. ---
31  2009 Probing the specifics of substrate binding for cytochrome c oxidase: a computer assisted approach. COX
32  2008 Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. EP, QM/MM
33  2008 Characterization of enzyme motions by solution NMR relaxation dispersion. CPMG, EP, RNase A, TIM
34  2008 Transient kinetic studies of pH-dependent hydrolyses by exo-type carboxypeptidase P on a 27-MHz quartz crystal microbalance. cat, QCM
35  2008 Transient kinetic studies of protein hydrolyses by endo- and exo-proteases on a 27 MHz quartz-crystal microbalance. ---
36  2007 A phage antibody to the active site of human placental alkaline phosphatase with higher affinity to the enzyme-substrate complex. AP, PLAP, pNPP
37  2007 Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B. RTKs
38  2007 Spectroscopic and electronic structure study of the enzyme-substrate complex of intradiol dioxygenases: substrate activation by a high-spin ferric non-heme iron site. 3,4-PCD, CD, LMCT, MCD, PCA
39  2006 Molecular Modeling the Reaction Mechanism of Serine-Carboxyl Peptidases. TI
40  2006 Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase. 2AP, T-T, T4-pdg
41  2004 Regulation of enzyme-substrate complexation by a substrate conjugated with a phospholipid polymer. AAP, HPPA, HRP
42  2003 A method for determining two substrates binding in the same active site of cytochrome P450BM3: an explanation of high energy omega product formation. ---
43  2003 Catalytic properties of an endogenous beta-lactamase responsible for the resistance of Azospirillum lipoferum to beta-lactam antibiotics. cat
44  2003 Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process. ---
45  2002 Kinetic properties of the enzyme-substrate system: a basis for immediate temperature compensation. ---
46  2002 Thermodynamic and activation parameters for the hydrolysis of amylose with Bacillus alpha-amylases in a diluted anionic surfactant solution. CMC, SDS
47  2001 Cobalt(II) and copper(II) binding of Bacillus cereus trinuclear phospholipase C: a novel 1H NMR spectrum of a 'Tri-Cu(II)' center in protein. ---
48  1998 Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs. ---
49  1996 Inhibition patterns of a model complex mimicking the reductive half-reaction of sulphite oxidase. EI, ESI
50  1996 Purification of a mammalian homologue of Escherichia coli endonuclease III: identification of a bovine pyrimidine hydrate-thymine glycol DNAse/AP lyase by irreversible cross linking to a thymine glycol-containing oligoxynucleotide. ---
51  1995 Kinetic characterization of enzyme forms involved in metal ion activation and inhibition of myo-inositol monophosphatase. ---
52  1994 Kinetics of hydrolysis of dansyl peptide substrates by thermolysin: analysis of fluorescence changes and determination of steady-state kinetic parameters. ---
53  1993 A physical assay for and kinetic analysis of the interactions between M1 RNA and tRNA precursor substrates. ---
54  1993 Evidence for retention of biological activity of a non-heme iron enzyme adsorbed on a silver colloid: a surface-enhanced resonance Raman scattering study. CCD, EI, RRS, SERRS, TCC
55  1987 Free energy differences between enzyme bound states. EP
56  1987 pH Effects on the Activity and Regulation of the NAD Malic Enzyme. ---
57  1983 Halogenated protocatechuates as substrates for protocatechuate dioxygenase from Pseudomonas cepacia. ---
58  1982 Clofibric acid and phenylpyruvic acid as biochemical probes for studying soluble bovine liver branched chain ketoacid dehydrogenase. ESI
59  1979 Determination of enzyme mechanisms by radiationless energy transfer kinetics. RET