Application of site-identification by ligand competitive saturation in computer-aided drug design
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Title
Application of site-identification by ligand competitive saturation in computer-aided drug design
Authors
Keywords
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Journal
NEW JOURNAL OF CHEMISTRY
Volume 46, Issue 3, Pages 919-932
Publisher
Royal Society of Chemistry (RSC)
Online
2021-11-30
DOI
10.1039/d1nj04028f
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Note: Only part of the references are listed.- Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics
- (2021) Richard D. Smith et al. Journal of Chemical Information and Modeling
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- (2021) Anderson A. Gomes et al. Journal of Chemical Information and Modeling
- Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation
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- (2021) Keisuke Yanagisawa et al. Journal of Chemical Information and Modeling
- Mixed‐solvent molecular dynamics simulation‐based discovery of a putative allosteric site on regulator of G protein signaling 4
- (2021) Wallace K. B. Chan et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Insights into substrate recognition and specificity for IgG by Endoglycosidase S2
- (2021) Asaminew H. Aytenfisu et al. PLoS Computational Biology
- Species-Specific Endotoxin Stimulus Determines Toll-Like Receptor 4- and Caspase 11-Mediated Pathway Activation Characteristics
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- Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)
- (2020) Alexander D. MacKerell et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations
- (2020) Gerard Martinez-Rosell et al. Journal of Chemical Information and Modeling
- Assessment of Binding Affinity via Alchemical Free Energy Calculations
- (2020) Maximilian Kuhn et al. Journal of Chemical Information and Modeling
- Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors
- (2020) Gudong Li et al. Journal of Chemical Information and Modeling
- The rise of molecular simulations in fragment-based drug design (FBDD): an overview
- (2020) Maicol Bissaro et al. DRUG DISCOVERY TODAY
- Rigorous Free Energy Simulations in Virtual Screening
- (2020) Zoe Cournia et al. Journal of Chemical Information and Modeling
- Straightforward Incorporation of Multiple Ligand Types into Molecular Dynamics Simulations for Efficient Binding Site Detection and Characterization
- (2020) Yaw Sing Tan et al. Journal of Chemical Theory and Computation
- Computational Characterization of Antibody–Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach
- (2020) Sunhwan Jo et al. MOLECULAR PHARMACEUTICS
- Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations
- (2020) Mahdi Mousaei et al. Journal of Chemical Information and Modeling
- Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics
- (2020) E. Prabhu Raman et al. Journal of Chemical Theory and Computation
- Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS)
- (2020) Sandeep Somani et al. JOURNAL OF PHARMACEUTICAL SCIENCES
- Ranking Reversible Covalent Drugs: From Free Energy Perturbation to Fragment Docking
- (2019) Han Zhang et al. Journal of Chemical Information and Modeling
- Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design
- (2019) Marc O’Reilly et al. DRUG DISCOVERY TODAY
- Hotspot Identification on Protein Surfaces Using Probe-Based MD Simulations: Successes and Challenges
- (2019) Abdallah Sayyed-Ahmad CURRENT TOPICS IN MEDICINAL CHEMISTRY
- Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization
- (2019) Vincent D. Ustach et al. Journal of Chemical Information and Modeling
- Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations
- (2019) Phani Ghanakota et al. Journal of Chemical Information and Modeling
- Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design
- (2019) Denis Schmidt et al. Journal of Chemical Theory and Computation
- Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ-Dynamics
- (2019) Amr H. Mahmoud et al. Journal of Chemical Theory and Computation
- Using AMBER18 for Relative Free Energy Calculations
- (2019) Lin Frank Song et al. Journal of Chemical Information and Modeling
- Cosolvent-Based Protein Pharmacophore for Ligand Enrichment in Virtual Screening
- (2019) Juan Pablo Arcon et al. Journal of Chemical Information and Modeling
- Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations
- (2019) Ji Young Lee et al. PROTEIN SCIENCE
- The NISTmAb Reference Material 8671 value assignment, homogeneity, and stability
- (2018) John E. Schiel et al. ANALYTICAL AND BIOANALYTICAL CHEMISTRY
- Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics
- (2018) Sarah E. Graham et al. Journal of Chemical Information and Modeling
- MixMD Probeview: Robust Binding Site Prediction from Cosolvent Simulations
- (2018) Sarah E. Graham et al. Journal of Chemical Information and Modeling
- ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation
- (2018) Kazuhiro Takemura et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics
- (2018) Jonah Z. Vilseck et al. Journal of Physical Chemistry Letters
- The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization
- (2018) Qian Dong et al. mAbs
- Modeling of Halogen–Protein Interactions in Co-Solvent Molecular Dynamics Simulations
- (2018) Ying Yang et al. Journal of Chemical Information and Modeling
- Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology
- (2018) Wenbo Yu et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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- (2017) Juan Pablo Arcon et al. Journal of Chemical Information and Modeling
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- (2017) S. Roy Kimura et al. Journal of Chemical Information and Modeling
- Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
- (2017) Zoe Cournia et al. Journal of Chemical Information and Modeling
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- Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems
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- Identifying binding hot spots on protein surfaces by mixed-solvent molecular dynamics: HIV-1 protease as a test case
- (2015) Peter M. U. Ung et al. BIOPOLYMERS
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- (2015) Sirish Kaushik Lakkaraju et al. Journal of Chemical Information and Modeling
- Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules
- (2015) Wenbo Yu et al. Journal of Chemical Information and Modeling
- The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions
- (2015) Yaw Sing Tan et al. Journal of Chemical Theory and Computation
- Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
- (2015) Thom Vreven et al. JOURNAL OF MOLECULAR BIOLOGY
- Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
- (2015) Lingle Wang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
- (2015) Dima Kozakov et al. Nature Protocols
- Binding hotspots on K-ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
- (2015) Priyanka Prakash et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
- (2015) Priyanka Prakash et al. PLoS Computational Biology
- Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method
- (2015) Chao-Yie Yang PLoS One
- Search strategies and evaluation in protein–protein docking: principles, advances and challenges
- (2014) Sheng-You Huang DRUG DISCOVERY TODAY
- The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations
- (2014) Yaw Sing Tan et al. Journal of Chemical Information and Modeling
- Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations
- (2014) Sirish Kaushik Lakkaraju et al. Journal of Chemical Theory and Computation
- Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
- (2014) Wenbo Yu et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites
- (2014) Daniel Alvarez-Garcia et al. JOURNAL OF MEDICINAL CHEMISTRY
- Rings in Drugs
- (2014) Richard D. Taylor et al. JOURNAL OF MEDICINAL CHEMISTRY
- The therapeutic monoclonal antibody market
- (2014) Dawn M Ecker et al. mAbs
- Therapeutic protein aggregation: mechanisms, design, and control
- (2014) Christopher J. Roberts TRENDS IN BIOTECHNOLOGY
- Structured Water Molecules in the Binding Site of Bromodomains Can Be Displaced by Cosolvent
- (2013) Danzhi Huang et al. ChemMedChem
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- (2013) Katrina W. Lexa et al. Journal of Chemical Information and Modeling
- Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach
- (2013) E. Prabhu Raman et al. Journal of Chemical Information and Modeling
- Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
- (2012) K. Vanommeslaeghe et al. Journal of Chemical Information and Modeling
- Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
- (2012) Ahmet Bakan et al. Journal of Chemical Theory and Computation
- Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations
- (2012) Wenbo Yu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- FTMAP: extended protein mapping with user-selected probe molecules
- (2012) C. H. Ngan et al. NUCLEIC ACIDS RESEARCH
- Analysis of Flexibility and Hotspots in Bcl-xL and Mcl-1 Proteins for the Design of Selective Small-Molecule Inhibitors
- (2012) Chao-Yie Yang et al. ACS Medicinal Chemistry Letters
- Protein–excipient interactions: Mechanisms and biophysical characterization applied to protein formulation development
- (2011) Tim J. Kamerzell et al. ADVANCED DRUG DELIVERY REVIEWS
- Small Molecule Binding to Proteins: Affinity and Binding/Unbinding Dynamics from Atomistic Simulations
- (2011) Danzhi Huang et al. ChemMedChem
- Predicting solution aggregation rates for therapeutic proteins: Approaches and challenges
- (2011) Christopher J. Roberts et al. INTERNATIONAL JOURNAL OF PHARMACEUTICS
- Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations
- (2011) E. Prabhu Raman et al. Journal of Chemical Information and Modeling
- Pharmer: Efficient and Exact Pharmacophore Search
- (2011) David Ryan Koes et al. Journal of Chemical Information and Modeling
- Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library
- (2011) Brian G. Pierce et al. PLoS One
- Hydrophobic Binding Hot Spots of Bcl-xL Protein−Protein Interfaces by Cosolvent Molecular Dynamics Simulation
- (2011) Chao-Yie Yang et al. ACS Medicinal Chemistry Letters
- Pharmacophore modeling and applications in drug discovery: challenges and recent advances
- (2010) Sheng-Yong Yang DRUG DISCOVERY TODAY
- Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping
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- (2010) Gary Walsh NATURE BIOTECHNOLOGY
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- Binding Site Detection and Druggability Index from First Principles
- (2009) Jesus Seco et al. JOURNAL OF MEDICINAL CHEMISTRY
- Three-Dimensional Pharmacophore Methods in Drug Discovery
- (2009) Andrew R. Leach et al. JOURNAL OF MEDICINAL CHEMISTRY
- Epitope Mapping of Anti-Interleukin-13 Neutralizing Antibody CNTO607
- (2009) Alexey Teplyakov et al. JOURNAL OF MOLECULAR BIOLOGY
- Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation
- (2009) Olgun Guvench et al. PLoS Computational Biology
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
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