Targeting cryptic-orthosteric site of PD-L1 for inhibitor identification using structure-guided approach

References

Page 1

	Year	Citations
VMD: Visual molecular dynamics William Humphrey, Andrew Dalke, Klaus Schulten Journal of Molecular Graphics EngineeringVisual Molecular DynamicsMolecular BiologyComputational ChemistryMolecular Dynamics	1996	64.1K
Development and testing of a general amber force field Junmei Wang, Romain M. Wolf, James W. Caldwell, Journal of Computational Chemistry Crystal StructureEngineeringAmber Force FieldsComputational ChemistryChemistry	2004	18.8K
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB James Maier, Carmenza Martinez, Koushik Kasavajhala, Journal of Chemical Theory and Computation Structural BioinformaticsBiomolecular Structure PredictionAmber Ff12sb ParameterMolecular BiologyProtein Side Chain	2015	10.6K
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data Daniel R. Roe, Thomas E. Cheatham Journal of Chemical Theory and Computation EngineeringMolecular BiologyAmber PackageComputational ChemistryMolecular Dynamics	2013	7.3K
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes Richard A. Friesner, Robert B. Murphy, Matthew P. Repasky, Journal of Medicinal Chemistry	2006	6.7K
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments G. Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Journal of Computer-Aided Molecular Design Virtual ScreeningHit IdentificationDrug TargetBiochemistryVirtual Screening Enrichments	2013	5.8K
Engagement of the Pd-1 Immunoinhibitory Receptor by a Novel B7 Family Member Leads to Negative Regulation of Lymphocyte Activation Gordon J. Freeman, Andrew J. Long, Yoshiko Iwai, The Journal of Experimental Medicine	2000	5.2K
<i>MMPBSA.py</i>: An Efficient Program for End-State Free Energy Calculations Bill R. Miller, T. Dwight McGee, Jason Swails, Journal of Chemical Theory and Computation	2012	4.3K
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules David A. Pearlman, David A. Case, James W. Caldwell, Computer Physics Communications EngineeringNormal Mode AnalysisNatural SciencesMolecular PropertyMolecular Biology	1995	3.1K
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins Edward Harder, Wolfgang Damm, Jon R. Maple, Journal of Chemical Theory and Computation Drug TargetDrug TargetingDrug-like Small MoleculesBiochemistryProtein Folding	2015	3K

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