Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin.

scientific article published on 23 March 2007

Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1529/BIOPHYSJ.106.099150
P932PMC publication ID1877793
P698PubMed publication ID17384076
P5875ResearchGate publication ID6423612

P50authorYe MeiQ50980178
John Z. H. ZhangQ68686424
P2093author name stringEmilia L Wu
KeLi Han
P2860cites workMolecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activationQ24337851
Design and synthesis of potent and selective macrocyclic thrombin inhibitorsQ27641704
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segmentQ27700069
Design and Synthesis of a Series of Potent and Orally Bioavailable Noncovalent Thrombin Inhibitors That Utilize Nonbasic Groups in the P1 PositionQ27765106
The coagulation cascade: initiation, maintenance, and regulationQ28610148
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.Q30333153
Thrombin structure and function: why thrombin is the primary target for antithromboticsQ36923198
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.Q43678172
Statistical molecular design, parallel synthesis, and biological evaluation of a library of thrombin inhibitorsQ43755650
Synthesis of novel thrombin inhibitors. Use of ring-closing metathesis reactions for synthesis of P2 cyclopentene- and cyclohexenedicarboxylic acid derivativesQ44368096
Synthesis and SAR of thrombin inhibitors incorporating a novel 4-amino-morpholinone sscaffold: analysis of X-ray crystal structure of enzyme inhibitor complexQ44572289
Discovery and evaluation of potent P1 aryl heterocycle-based thrombin inhibitorsQ44910563
Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complexQ44988987
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.Q45952403
In-depth study of tripeptide-based alpha-ketoheterocycles as inhibitors of thrombin. Effective utilization of the S1' subsite and its implications to structure-based drug designQ46383079
Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.Q46403165
Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutationsQ46661986
New Advance in Computational Chemistry:  Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction EnergyQ47687041
A new quantum method for electrostatic solvation energy of proteinQ51134805
Beyond the benzene dimer: an investigation of the additivity of pi-pi interactionsQ51937909
Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulationsQ52065973
Thrombin-induced chemotaxis and aggregation of neutrophilsQ69593060
Functionality map analysis of the active site cleft of human thrombinQ71483760
Design of highly potent noncovalent thrombin inhibitors that utilize a novel lipophilic binding pocket in the thrombin active siteQ73183249
Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response methodQ73346494
Thrombotic Complications of Antithrombotic Therapy: A Paradox with Implications for Clinical PracticeQ73907400
Continuum solvent studies of the stability of RNA hairpin loops and helicesQ74532607
Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin,Q78162558
Fractionation of peptide with disulfide bond for quantum mechanical calculation of interaction energy with moleculesQ80368392
Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexesQ80427060
Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinaseQ81514871
P433issue12
P407language of work or nameEnglishQ1860
P304page(s)4244-4253
P577publication date2007-03-23
P1433published inBiophysical JournalQ2032955
P1476titleQuantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin
P478volume92

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cites work (P2860)
Q41010244A quantum biochemistry investigation of willardiine partial agonism in AMPA receptors.
Q47400790A theoretical insight into selectivity of inhibitors toward two domains of bromodomain-containing protein 4 using molecular dynamics simulations.
Q47629500Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations
Q39960733Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation
Q35783809Interaction of I50V Mutant and I50L/A71V Double Mutant HIV-Protease with Inhibitor TMC114 (Darunavir): Molecular Dynamics Simulation and Binding Free Energy Studies
Q58710194Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5
Q51477064Predicting bioactive conformations and binding modes of macrocycles
Q38028650Quantum mechanical effect in protein–ligand interaction
Q48359993Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling.

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