相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Quantitatively Accounting for Protein Reorganization in Computer-Aided Drug Design
Mikolai Fajer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2023)
Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers
Vladimir Mironov et al.
CHEMISTRY-A EUROPEAN JOURNAL (2022)
Fragment molecular orbital calculations for biomolecules
Kaori Fukuzawa et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)
The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides
Vladimir Sladek et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)
Parametrized quantum-mechanical approaches combined with the fragment molecular orbital method
Dmitri G. Fedorov
JOURNAL OF CHEMICAL PHYSICS (2022)
Protein-ligand binding affinity prediction of cyclin-dependent kinase-2 inhibitors by dynamically averaged fragment molecular orbital-based interaction energy
Kenichiro Takaba et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2022)
Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G
Masayasu Fujii et al.
Chem-Bio Informatics Journal (2022)
1,4-Dideoxy-1,4-imino-d- and l-lyxitol-based inhibitors bind to Golgi α-mannosidase II in different protonation forms
Juraj Kona et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2022)
The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization
Taiji Nakamura et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2022)
Binding kinetics of liposome conjugated E-selectin and P-selectin glycoprotein ligand-1 measured with atomic force microscopy
Yuyuan Zhou et al.
COLLOIDS AND SURFACES B-BIOINTERFACES (2021)
Insights into Selectin Inhibitor Design from Endogenous Isomeric Ligands of SLea and SLex
Zhicheng Hu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)
Rational Design of Novel Glycomimetic Peptides for E-Selectin Targeting
Veronica A. Jimenez et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)
The fragment molecular orbital method combined with density-functional tight-binding and periodic boundary conditions
Yoshio Nishimoto et al.
JOURNAL OF CHEMICAL PHYSICS (2021)
Dynamic Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method
Shigenori Tanaka et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Quantum Mechanics Helps Uncover Atypical Recognition Features in the Flavin Mononucleotide Riboswitch
Indrajit Deb et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems
Taiji Nakamura et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2021)
pyProGA-A PyMOL plugin for protein residue network analysis
Vladimir Sladek et al.
PLOS ONE (2021)
Hot Spot Analysis of YAP-TEAD Protein-Protein Interaction Using the Fragment Molecular Orbital Method and Its Application for Inhibitor Discovery
Jongwan Kim et al.
CANCERS (2021)
Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study
Pavel Smak et al.
GLYCOBIOLOGY (2021)
Functional binding of E-selectin to its ligands is enhanced by structural features beyond its lectin domain
Fajr A. Aleisa et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2020)
Recent developments in the general atomic and molecular electronic structure system
Giuseppe M. J. Barca et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review
Igor Tvaroska et al.
MOLECULES (2020)
Insights into the Loop at the E-Selectin Binding Site: From Open to Close Conformation
Xiaocong Wang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Partition Analysis for Density-Functional Tight-Binding
Dmitri G. Fedorov
JOURNAL OF PHYSICAL CHEMISTRY A (2020)
How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP3-in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5′ thio galactose substrates
J. Kona
ORGANIC & BIOMOLECULAR CHEMISTRY (2020)
Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method
Shigenori Tanaka et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2020)
A 3D-QSAR Analysis of CDK2 Inhibitors Using FMO Calculations and PLS Regression
Tomoki Yoshida et al.
CHEMICAL & PHARMACEUTICAL BULLETIN (2019)
Solvent Screening in Zwitterions Analyzed with the Fragment Molecular Orbital Method
Dmitri G. Fedorov
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Glycans in drug discovery
Pablo Valverde et al.
MEDCHEMCOMM (2019)
Molecular association model of PPAR alpha and its new specific and efficient ligand, pemafibrate: Structural basis for SPPARM alpha
Yuta Yamamoto et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2018)
Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics
Dmitri G. Fedorov et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2018)
Protein Residue Networks from Energetic and Geometric Data: Are They Identical?
Vladimir Sladek et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Binding free energy calculations on E-selectin complexes with sLex oligosaccharide analogs
Pabla A. Barra et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2017)
DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information
Kai Cheng et al.
GLYCOBIOLOGY (2017)
Glycan Bound to the Selectin Low Affinity State Engages Glu-88 to Stabilize the High Affinity State under Force
Padmaja Mehta-D'souza et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2017)
Three-Body Expansion of the Fragment Molecular Orbital Method Combined with Density-Functional Tight-Binding
Yoshio Nishimoto et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
PSGL-1: A New Player in the Immune Checkpoint Landscape
Roberto Tinoco et al.
TRENDS IN IMMUNOLOGY (2017)
The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications
Dmitri G. Fedorov
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2017)
E-selectin ligand complexes adopt an extended high-affinity conformation
Roland C. Preston et al.
JOURNAL OF MOLECULAR CELL BIOLOGY (2016)
Discovery of New E-Selectin Inhibitors by Virtual Screening, Fluorescence Binding Assays, and STD NMR Experiments
Pabla A. Barra et al.
CHEMMEDCHEM (2016)
Subsystem Analysis for the Fragment Molecular Orbital Method and Its Application to Protein-Ligand Binding in Solution
Dmitri G. Fedorov et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2016)
Selectins: initiators of leucocyte adhesion and signalling at the vascular wall
Rodger P. McEver
CARDIOVASCULAR RESEARCH (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method
Yoshio Nishimoto et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems
Shigenori Tanaka et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
Parametrization and Benchmark of DFTB3 for Organic Molecules
Michael Gaus et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
G. Madhavi Sastry et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)
Understanding Selectin Counter-Receptor Binding from Electrostatic Energy Computations and Experimental Binding Studies
Anna Lena Woelke et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Nanomolar E-Selectin Antagonists with Prolonged Half-Lives by a Fragment-Based Approach
Jonas Egger et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
An overview of the Amber biomolecular simulation package
Romelia Salomon-Ferrer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)
Sialyl Lewisx: A Pre-Organized Water Oligomer?
Florian P. C. Binder et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2012)
Development of the four-body corrected fragment molecular orbital (FMO4) method
Tatsuya Nakano et al.
CHEMICAL PHYSICS LETTERS (2012)
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
Mark S. Gordon et al.
CHEMICAL REVIEWS (2012)
Effect of the Damping Function in Dispersion Corrected Density Functional Theory
Stefan Grimme et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Selectin inhibitors: a patent review
Patricia W. Bedard et al.
EXPERT OPINION ON THERAPEUTIC PATENTS (2010)
Role of the Key Mutation in the Selective Binding of Avian and Human Influenza Hemagglutinin to Sialosides Revealed by Quantum-Mechanical Calculations
Toshihiko Sawada et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Selectins promote tumor metastasis
Heinz Laeubli et al.
SEMINARS IN CANCER BIOLOGY (2010)
Glycosylation in immune cell trafficking
Markus Sperandio et al.
IMMUNOLOGICAL REVIEWS (2009)
Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy
Toshio Watanabe et al.
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE (2009)
Lymphocytes in the Peritoneum Home to the Omentum and Are Activated by Resident Dendritic Cells
Douglas A. Carlow et al.
JOURNAL OF IMMUNOLOGY (2009)
From carbohydrate leads to glycomimetic drugs
Beat Ernst et al.
NATURE REVIEWS DRUG DISCOVERY (2009)
Structural basis for selectin mechanochemistry
Timothy A. Springer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Replacing a lectin domain residue in L-selectin enhances binding to P-selectin glycoprotein ligand-1 but not to 6-sulfo-sialyl Lewis x
Arkadiusz G. Klopocki et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2008)
GLYCAM06: A generalizable Biomolecular force field. Carbohydrates
Karl N. Kirschner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Performance of spin-component-scaled Moller-Plesset theory (SCS-MP2) for potential energy curves of noncovalent interactions
Tait Takatani et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2007)
DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations
Toshio Watanabe et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Is spin-component scaled second-order moller-plesset perturbation theory an appropriate method for the study of noncovalent interactions in molecules?
Jens Antony et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2007)
Pair interaction energy decomposition analysis
Dmitri G. Fedorov et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Getting to the site of inflammation: the leukocyte adhesion cascade updated
Klaus Ley et al.
NATURE REVIEWS IMMUNOLOGY (2007)
Glycosylation in cellular mechanisms of health and disease
Kazuaki Ohtsubo et al.
CELL (2006)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Quinic acid derivatives as sialyl Lewisx-mimicking selectin inhibitors:: Design, synthesis, and crystal structure in complex with E-selectin
N Kaila et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
The importance of three-body terms in the fragment molecular orbital method
DG Fedorov et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
The discovery, biology, and drug development of sialyl Lea and sialyl Lex
JL Magnani
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2004)
Model glycosulfopeptides from P-selectin glycoprotein ligand-1 require tyrosine sulfation and a core 2-branched O-glycan to bind to L-selectin
A Leppänen et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2003)
The role of selectins in inflammation and disease
K Ley
TRENDS IN MOLECULAR MEDICINE (2003)
Improved second-order Moller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies
S Grimme
JOURNAL OF CHEMICAL PHYSICS (2003)
Selectin inhibitors
N Kaila et al.
EXPERT OPINION ON THERAPEUTIC PATENTS (2003)
Design and synthesis of sialyl Lewisx mimics as E- and P-selectin inhibitors
N Kaila et al.
MEDICINAL RESEARCH REVIEWS (2002)
Glycosylation in the control of selectin counter-receptor structure and function
JB Lowe
IMMUNOLOGICAL REVIEWS (2002)
Binding of glycosulfopeptides to P-selectin requires stereospecific contributions of individual tyrosine sulfate and sugar residues
A Leppänen et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2000)
Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLeX and PSGL-1
WS Somers et al.
CELL (2000)
Study on selectin blocker. 8. Lead discovery of a non-sugar antagonist using a 3D-pharmacophore model
Y Hiramatsu et al.
JOURNAL OF MEDICINAL CHEMISTRY (2000)