Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

Cui, Qizhi; Sulea, Traian; Schrag, Joseph D.; Munger, Christine; Hung, Ming-Ni; Naïm, Marwen; Cygler, Miroslaw; Purisima, Enrico O.

doi:10.1016/j.jmb.2008.04.035

Cited by 168Protein Structure and DynamicsComputational Drug Discovery MethodsAdvanced Chemical Physics Studies

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

Cui, Qizhi, Sulea, Traian, Schrag, Joseph D., Munger, Christine, Hung, Ming-Ni, Naïm, Marwen, Cygler, Miroslaw, Purisima, Enrico O.·2008·Journal of Molecular Biology

DOI 10.1016/j.jmb.2008.04.035

Open this paper in CoChat — free account

Abstract

Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as model system, we explored a structure-based computational protocol to probe and characterize binding affinity hot spots at protein-protein interfaces. Hot spots are located by virtual alanine-scanning consensus predictions over three different energy functions and two different single-structure representations of the complex. Refined binding affinity predictions for select hot-spot mutations are carried out by applying first-principle methods such as the molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) to the molecular dynamics (MD) trajectories for mutated and wild-type complexes. Here, predicted hot-spot residues were actually mutated to alanine, and crystal structures of the mutated complexes were determined. Two mutated MP1-p14 complexes were investigated, the p14(Y56A)-mutated complex and the MP1(L63A,L65A)-mutated complex. Alternative ways to generate MD ensembles for mutant complexes, not relying on crystal structures for mutated complexes, were also investigated. The SIE function, fitted on protein-ligand binding affinities, gave absolute binding affinity predictions in excellent agreement with experiment and outperformed standard MM-GBSA predictions when tested on the MD ensembles of Ras-Raf and Ras-RalGDS protein-protein complexes. For wild-type and mutant MP1-p14 complexes, SIE predictions of relative binding affinities were supported by a yeast two-hybrid assay that provided semiquantitative relative interaction strengths. Results on the MP1-mutated complex suggested that SIE predictions deteriorate if mutant MD ensembles are approximated by just mutating the wild-type MD trajectory. The SIE data on the p14-mutated complex indicated feasibility for generating mutant MD ensembles from mutated wild-type crystal structure, despite local structural differences observed upon mutation. For energetic considerations, this would circumvent costly needs to produce and crystallize mutated complexes. The sensitized protein-protein interface afforded by the p14(Y56A) mutation identified here has practical applications in screening-based discovery of first-generation small-molecule hits for further development into specific modulators of the mitogen-activated protein kinase signaling pathway.

Integrity signals

Registry

Crossref · 10.1016/j.jmb.2008.04.035

Cites

56 of 56 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

The structures of LAMTOR2, LAMTOR3 and LAMTOR5 revealed roadblock folds for the individual LAMTOR3 and LAMTOR5 monomers and the formation of MP1/p14 heterodimers by edge-to-edge juxtaposition of the roadblock domains.
“The structures of LAMTOR2, LAMTOR3 and LAMTOR5 were the first to be characterized prior to the discovery of the Ragulator complex (Kurzbauer et al., 2004; Cui et al., 2008; Lunin et al., 2004; Qian et al., 2005; Garcia-Saez et al., 2011), revealing roadblock folds for the individual LAMTOR3 and LAMTOR5 monomers, and the formation of MP1/p14 heterodimers by edge-to-edge juxtaposition of the roadb”
From Signal integration in the (m)TORC1 growth pathway (2018) · cites this paper as Cui et al., 2008

The Protein Data Bank
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 38,335 · see citing works
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
Darden, T., York, D., & Pedersen, L. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464397 · Cited by 29,588 · see citing works
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581 · see citing works
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
Ryckaert, J., Ciccotti, G., & Berendsen, H. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 19,525 · see citing works
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,671 · see citing works
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535 · see citing works
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., et al. (2000) · Accounts of Chemical Research · doi:10.1021/ar000033j · Cited by 4,978 · see citing works
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T.-S., et al. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10349 · Cited by 4,271 · see citing works
MAP kinase signalling pathways in cancer
Dhillon, A. S., Hagan, S., Rath, O., & Kolch, W. (2007) · Oncogene · doi:10.1038/sj.onc.1210421 · Cited by 2,995 · see citing works
Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,883 · see citing works
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
Sitkoff, D. F., Sharp, K. A., & Honig, B. H. (1994) · The Journal of Physical Chemistry · doi:10.1021/j100058a043 · Cited by 2,160 · see citing works
Free energy calculations: Applications to chemical and biochemical phenomena
Kollman, P. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,131 · see citing works
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., & Case, D. A. (1998) · Journal of the American Chemical Society · doi:10.1021/ja981844+ · Cited by 1,634 · see citing works
The finer things in X-ray diffraction data collection
Pflugrath, J. W. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744499900935x · Cited by 1,244 · see citing works
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
Weiser, J., Shenkin, P. S., & Still, W. C. (1999) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(19990130)20:2 · Cited by 1,209 · see citing works
Modification of the Generalized Born Model Suitable for Macromolecules
Onufriev, A. V., Bashford, D., & Case, D. A. (2000) · The Journal of Physical Chemistry B · doi:10.1021/jp994072s · Cited by 1,093 · see citing works
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
Beveridge, D. L., & DiCapua, F. M. (1989) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.18.060189.002243 · Cited by 1,088 · see citing works
Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.
Gohlke, H., Kiel, C., & Case, D. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,087 · see citing works
Coordinating ERK/MAPK signalling through scaffolds and inhibitors
Kölch, W. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1743 · Cited by 1,070 · see citing works
Statistical Mechanics
(1977) · Springer eBooks · doi:10.1007/978-1-4615-7906-9 · Cited by 932 · see citing works
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
Gilson, M. K., & Honig, B. H. (1988) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340040104 · Cited by 855 · see citing works
Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf
Gohlke, H., & Case, D. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.10379 · Cited by 836 · see citing works
A simple physical model for binding energy hot spots in protein–protein complexes
Kortemme, T., & Baker, D. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202485799 · Cited by 801 · see citing works
Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies
Massova, I., & Kollman, P. A. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990935j · Cited by 778 · see citing works
Free energy calculations: a breakthrough for modeling organic chemistry in solution
Jorgensen, W. L. (1989) · Accounts of Chemical Research · doi:10.1021/ar00161a004 · Cited by 637 · see citing works
Integrating signals from RTKs to ERK/MAPK
Mckay, M., & Morrison, D. K. (2007) · Oncogene · doi:10.1038/sj.onc.1210394 · Cited by 616 · see citing works
Computational Alanine Scanning of Protein-Protein Interfaces
Kortemme, T., Kim, D. E., & Baker, D. A. (2004) · Science s STKE · doi:10.1126/stke.2192004pl2 · Cited by 586 · see citing works
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy–entropy compensation
Rekharsky, M. V., Mori, T., Yang, C., Ko, Y. H., Selvapalam, N., Kim, H., Sobransingh, D., Kaifer, A. E., Liu, S., Isaacs, L., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706407105 · Cited by 583 · see citing works
Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space
Naïm, M., Bhat, S., Rankin, K. N., Dennis, S., Chowdhury, S. F., Siddiqi, M. I., Drabik, P., Sulea, T. I., Bayly, C. I., Jakalian, A., et al. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci600406v · Cited by 420 · see citing works
Self-citation
Phase I and Pharmacodynamic Study of the Oral MEK Inhibitor CI-1040 in Patients With Advanced Malignancies
LoRusso, P. M., Adjei, A. A., Varterasian, M. L., Gadgeel, S. M., Reid, J. M., Mitchell, D. Y., Hanson, L. J., DeLuca, P., Bruzek, L. M., Piens, J., et al. (2005) · Journal of Clinical Oncology · doi:10.1200/jco.2005.14.415 · Cited by 402 · see citing works
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
Wang, W., & Kollman, P. A. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4057 · Cited by 322 · see citing works
Computational alanine scanning of the 1:1 human growth hormone–receptor complex
Huo, S., Massova, I., & Kollman, P. A. (2001) · Journal of Computational Chemistry · doi:10.1002/jcc.1153 · Cited by 305 · see citing works
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
Field, M. J., Albe, M., Bret, C., Martin, F. P.-D., & Thomas, A. M. (2000) · Journal of Computational Chemistry · doi:10.1002/1096-987x(200009)21:12 · Cited by 303 · see citing works
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
Deng, Y., & Roux, B. (2006) · Journal of Chemical Theory and Computation · doi:10.1021/ct060037v · Cited by 289 · see citing works
On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute−Solvent Interaction Energy
Levy, R. M., Zhang, L. Y., Gallicchio, E., & Felts, A. K. (2003) · Journal of the American Chemical Society · doi:10.1021/ja029833a · Cited by 284 · see citing works
Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
Lee, M. C., & Duan, Y. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10470 · Cited by 275 · see citing works
The Kinase Inhibitor Sorafenib Induces Cell Death through a Process Involving Induction of Endoplasmic Reticulum Stress
Rahmani, M., Davis, E. M., Crabtree, T. R., Habibi, J. R., Nguyen, T. K., Dent, P., & Grant, S. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01080-06 · Cited by 242 · see citing works
Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design
Chen, W., Chang, C. A., & Gilson, M. K. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.049494 · Cited by 241 · see citing works
Computer Simulation of Protein−Protein Interactions
Elcock, A. H., Sept, D., & McCammon, J. A. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp003602d · Cited by 214 · see citing works
Study of the insulin dimerization: Binding free energy calculations and per‐residue free energy decomposition
Zoete, V., Meuwly, M., & Karplus, M. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20528 · Cited by 212 · see citing works
A simple yet accurate boundary element method for continuum dielectric calculations
Purisima, E. O., & Nilar, S. (1995) · Journal of Computational Chemistry · doi:10.1002/jcc.540160604 · Cited by 150 · see citing works
Self-citation
Comparison between computational alanine scanning and per‐residue binding free energy decomposition for protein–protein association using MM‐GBSA: Application to the TCR‐p‐MHC complex
Zoete, V., & Michielin, O. A. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21395 · Cited by 123 · see citing works
Change in protein flexibility upon complex formation: Analysis of Ras‐Raf using molecular dynamics and a molecular framework approach
Gohlke, H., Kuhn, L. A., & Case, D. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20116 · Cited by 114 · see citing works
Imaging polysaccharides by atomic force microscopy
Kirby, A. R., Gunning, A. P., & Morris, V. J. (1998) · Biopolymers · doi:10.1002/(sici)1097-0282(199603)38:3 · Cited by 107 · see citing works
Fast summation boundary element method for calculating solvation free energies of macromolecules
Purisima, E. O. (1998) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199810)19:13 · Cited by 104 · see citing works
Self-citation
Crystal structure of the p14/MP1 scaffolding complex: How a twin couple attaches mitogen-activated protein kinase signaling to late endosomes
Kurzbauer, R., Teis, D., de Araujo, M. E. G., Maurer-Stroh, S., Eisenhaber, F., Bourenkov, G. P., Bartunik, H. D., Hekman, M., Rapp, U. R., Huber, L. A., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403435101 · Cited by 95 · see citing works
Effects of Sorafenib on Symptoms and Quality of Life
Bukowski, R. M., Cella, D. F., Gondek, K., & Escudier, B. J. (2007) · American Journal of Clinical Oncology · doi:10.1097/01.coc.0000258732.80710.05 · Cited by 89 · see citing works
Thermodynamics of Ras/Effector and Cdc42/Effector Interactions Probed by Isothermal Titration Calorimetry
Rudolph, M. G., Linnemann, T., Grünewald, P., Wittinghofer, A., Vetter, I. R., & Herrmann, C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m011600200 · Cited by 71 · see citing works
The Structure of the MAPK Scaffold, MP1, Bound to Its Partner, p14
Lunin, V. V., Munger, C., Wagner, J., Ye, Z., Cygler, M., & Sacher, M. G. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m401648200 · Cited by 67 · see citing works
Self-citation
Computational analysis of binding of P1 variants to trypsin
Brandsdal, B. O., Åqvist, J., & Smalås, A. O. (2001) · Protein Science · doi:10.1110/ps.940101 · Cited by 57 · see citing works
Molecular surface generation using a variable‐radius solvent probe
Bhat, S., & Purisima, E. O. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20682 · Cited by 52 · see citing works
Self-citation
On the transferability of hydration‐parametrized continuum electrostatics models to solvated binding calculations
Rankin, K. N., Sulea, T. I., & Purisima, E. O. (2003) · Journal of Computational Chemistry · doi:10.1002/jcc.10261 · Cited by 25 · see citing works
Self-citation
ADAPT: A molecular mechanics approach for studying the structural properties of long DNA sequences
Lafontaine, I., & Lavery, R. (2000) · Biopolymers · doi:10.1002/1097-0282(2000)56:4 · Cited by 21 · see citing works
A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme
Chandra, N. R., Muirhead, H., Holbrook, J. J., Bernstein, B., Hol, W. G. J., & Sessions, R. B. (1998) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19980301)30:4 · Cited by 11 · see citing works

Flagged first, then by citations

Sorted by citations

Variability in docking success rates due to dataset preparation.
Corbeil, C. R., Williams, C. I., & Labute, P. (2012) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-012-9570-1 · Cited by 469 · see citing works
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface
Metz, A., Pfleger, C., Kopitz, H., Pfeiffer‐Marek, S., Baringhaus, K. H., & Gohlke, H. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci200322s · Cited by 123 · see citing works
Exploring the Potentiality of Natural Products from Essential Oils as Inhibitors of Odorant-Binding Proteins: A Structure- and Ligand-Based Virtual Screening Approach To Find Novel Mosquito Repellents
da Costa, K. S., Galúcio, J. M. P., da Costa, C. H. S., Santana, A. R., Carvalho, V. D. S., do Nascimento, L. D., Lima, A. H., Cruz, J. N., Alves, C. N., & Lameira, J. (2019) · ACS Omega · doi:10.1021/acsomega.9b03157 · Cited by 102 · see citing works
Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants
da Costa, C. H. S., de Freitas, C. A. B., Alves, C. N., & Lameira, J. (2022) · Scientific Reports · doi:10.1038/s41598-022-12479-9 · Cited by 100 · see citing works
Huprine-tacrine heterodimers as anti-amyloidogenic compounds of potential interest against Alzheimer's and prion diseases.
Galdeano, C., Viayna, E., Sola, I., Formosa, X., Camps, P., Badía, A., Clos, M. V., Relat, J., Ratia, M., Bartolini, M., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm200840c · Cited by 91 · see citing works
Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction
Bradshaw, R. T., Patel, B. H., Tate, E. W., Leatherbarrow, R. J., & Gould, I. R. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq047 · Cited by 83 · see citing works
Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation
Liu, H., & Yao, X. (2009) · Molecular Pharmaceutics · doi:10.1021/mp900131p · Cited by 82 · see citing works
Exploring the Size Limit of Templates for Inhibitors of the M2 Ion Channel of Influenza A Virus
Duque, M. D., Ma, C., Torres, E., Wang, J., Naesens, L. M. J., Juárez‐Jiménez, J., Camps, P., Luque, F. J., DeGrado, W. F., Lamb, R. A., et al. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm101334y · Cited by 76 · see citing works
Survey of the year 2008: applications of isothermal titration calorimetry
Falconer, R. J., Penkova, A., Jelesarov, I., & Collins, B. M. (2010) · Journal of Molecular Recognition · doi:10.1002/jmr.1025 · Cited by 74 · see citing works
Solvated Interaction Energy (SIE) for Scoring Protein–Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise
Sulea, T. I., Cui, Q., & Purisima, E. O. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci2000242 · Cited by 70 · see citing works
Self-citation
Ego3 Functions as a Homodimer to Mediate the Interaction between Gtr1-Gtr2 and Ego1 in the EGO Complex to Activate TORC1
Zhang, T., Gulli, M., Yang, H., VIRGILIO, C. D., & Ding, J. (2012) · Structure · doi:10.1016/j.str.2012.09.019 · Cited by 63 · see citing works
Small-Molecule Inhibitors of the Pseudaminic Acid Biosynthetic Pathway: Targeting Motility as a Key Bacterial Virulence Factor
Menard, R., Schoenhofen, I. C., Tao, L., Aubry, A. J., Bouchard, P., Reid, C. W., Lachance, P., Twine, S. M., Fulton, K. M., Cui, Q., et al. (2014) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.03858-14 · Cited by 52 · see citing works
Self-citation
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
May, A., Pool, R., van Dijk, E., Bijlard, J., Abeln, S., Heringa, J., & Feenstra, K. (2014) · Bioinform. · doi:10.1093/bioinformatics/btt675 · Cited by 51 · see citing works
1,2,3,4-Tetrahydrobenzo[h][1,6]naphthyridines as a new family of potent peripheral-to-midgorge-site inhibitors of acetylcholinesterase: Synthesis, pharmacological evaluation and mechanistic studies
Pietro, O. D., Viayna, E., Vicente‐García, E., Bartolini, M., Ramón, R., Juárez‐Jiménez, J., Clos, M. V., Pérez, B., Andrisano, V., Luque, F. J., et al. (2013) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2013.12.008 · Cited by 50 · see citing works
Copper-Transfer Mechanism from the Human Chaperone Atox1 to a Metal-Binding Domain of Wilson Disease Protein
Rodriguez-Granillo, A., Crespo, A., Estrin, D. A., & Wittung-Stafshede, P. E. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911208z · Cited by 49 · see citing works
Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation
Chen, J., Wang, J., Zhang, Q., Chen, K., & Zhu, W. (2015) · Scientific Reports · doi:10.1038/srep17421 · Cited by 49 · see citing works
Understanding the molecular basis of MK2–p38α signaling complex assembly: insights into protein–protein interaction by molecular dynamics and free energy studies
Yang, Y., Liu, H., & Yao, X. (2012) · Molecular BioSystems · doi:10.1039/c2mb25042j · Cited by 48 · see citing works
Purification and identification of metabolites produced by Bacillus cereus and B. subtilis active against Meloidogyne exigua, and their in silico interaction with a putative phosphoribosyltransferase fromM. incognita
de Oliveira, D. F., Júnior, H. M. D. S., Nunes, A. D. S., Campos, V. P., de Pinho, R. S. C., & Gajo, G. C. (2014) · Anais da Academia Brasileira de Ciências · doi:10.1590/0001-3765201402412 · Cited by 46 · see citing works
Understanding the molecular basis of agonist/antagonist mechanism of human mu opioid receptor through gaussian accelerated molecular dynamics method
Wang, Y., & Chan, Y. (2017) · Scientific Reports · doi:10.1038/s41598-017-08224-2 · Cited by 46 · see citing works
Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study
Kumar, A., Cocco, E. E., Atzori, L., Marrosu, M. G., & Pieroni, E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0059711 · Cited by 44 · see citing works
Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain
Anisimov, V. M., & Cavasotto, C. N. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21808 · Cited by 44 · see citing works
Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions
Chen, J. (2016) · RSC Advances · doi:10.1039/c6ra09201b · Cited by 44 · see citing works
Binding Modes of Three Inhibitors 8CA, F8A and I4A to A-FABP Studied Based on Molecular Dynamics Simulation
Chen, J., Wang, J., & Zhu, W. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099862 · Cited by 41 · see citing works
Probing the Structural and Energetic Basis of Kinesin–Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
Li, M., & Zheng, W. (2011) · Biochemistry · doi:10.1021/bi2008257 · Cited by 41 · see citing works
Scutellarin from Scutellaria baicalensis Suppresses Adipogenesis by Upregulating PPARα in 3T3-L1 Cells
Lu, K., Han, M., Ting, H. L., Liu, Z., & Zhang, D. (2013) · Journal of Natural Products · doi:10.1021/np300889y · Cited by 39 · see citing works
Molecular mechanism of HIV‐1 integrase–vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective
Xue, W., Liu, H., & Yao, X. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.22887 · Cited by 37 · see citing works
Exploring drug-resistant mechanisms of I84V mutation in HIV-1 protease toward different inhibitors by thermodynamics integration and solvated interaction energy method
Gao, Y., Zhu, T., & Chen, J. (2018) · Chemical Physics Letters · doi:10.1016/j.cplett.2018.06.040 · Cited by 37 · see citing works
The Solvated Interaction Energy Method for Scoring Binding Affinities
Sulea, T. I., & Purisima, E. O. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-465-0_19 · Cited by 36 · see citing works
Self-citation
Structural Basis for NHERF1 PDZ Domain Binding
Mamonova, T., Kurnikova, M. G., & Friedman, P. A. (2012) · Biochemistry · doi:10.1021/bi201213w · Cited by 35 · see citing works
Allosteric Noncompetitive Small Molecule Selective Inhibitors of CD45 Tyrosine Phosphatase Suppress T-Cell Receptor Signals and Inflammation In Vivo
Perron, M. D., Chowdhury, S. F., Aubry, I., Purisima, E. O., Tremblay, M. L., & Saragovi, H. U. (2014) · Molecular Pharmacology · doi:10.1124/mol.113.089847 · Cited by 35 · see citing works
Self-citation
Molecular dynamics study of small molecule inhibitors of the Bcl‐2 family
Acoca, S., Cui, Q., Shore, G. C., & Purisima, E. O. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23083 · Cited by 34 · see citing works
Self-citation
Stability of the Endosomal Scaffold Protein LAMTOR3 Depends on Heterodimer Assembly and Proteasomal Degradation
de Araújo, M. E. G., Stasyk, T., Taub, N., Ebner, H. L., Fürst, B., Filipek, P. A., Weys, S., Hess, M. W., Lindner, H. H., Kremser, L., et al. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.349480 · Cited by 33 · see citing works
Identification of new inhibitors against human Great wall kinase using in silico approaches
Ammarah, U., Kumar, A., Pal, R. R., Bal, N. C., & Misra, G. (2018) · Scientific Reports · doi:10.1038/s41598-018-23246-0 · Cited by 33 · see citing works
Ponatinib Is a Pan-BCR-ABL Kinase Inhibitor: MD Simulations and SIE Study
Tanneeru, K., & Guruprasad, L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078556 · Cited by 33 · see citing works
Transition metals tailoring of phosphorus-doped gallium nitride nanotubes as sensors for N-butenyl homoserine lactone (BHL): A computational study
Ekpong, B. O., Abdullah, H. Y., Emmanuel, E., Benjamin, I., & Agurokpon, D. C. (2024) · Computational and Theoretical Chemistry · doi:10.1016/j.comptc.2024.114914 · Cited by 32 · see citing works
Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge
Hogues, H., Sulea, T. I., & Purisima, E. O. (2014) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-014-9715-5 · Cited by 32 · see citing works
Self-citation
Structural Analysis of Viral Infectivity Factor of HIV Type 1 and Its Interaction with A3G, EloC and EloB
da Costa, K. S., Leal, E. D. S., dos Santos, A. M., Lima, A. H., Alves, C. N., & Lameira, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089116 · Cited by 31 · see citing works
Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation
Rodriguez-Granillo, A., Sedlák, E., & Wittung-Stafshede, P. E. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.07.065 · Cited by 31 · see citing works
The molecular basis of IGF-II/IGF2R recognition: a combined molecular dynamics simulation, free-energy calculation and computational alanine scanning study
Guo, J., Wang, X., Sun, H., Liu, H., & Yao, X. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1159-4 · Cited by 31 · see citing works
Assessment of Solvated Interaction Energy Function for Ranking Antibody–Antigen Binding Affinities
Sulea, T. I., Vivcharuk, V., Corbeil, C. R., Deprez, C., & Purisima, E. O. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00043 · Cited by 29 · see citing works
Self-citation
DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling.
Ojha, A. A., Thakur, S., Ahn, S.-H., & Amaro, R. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00282 · Cited by 25 · see citing works
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
Anisimov, V. M., Žiemys, A., Kizhake, S., Yuan, Z., Natarajan, A., & Cavasotto, C. N. (2011) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9484-3 · Cited by 28 · see citing works
Structure–activity relationships of fraxamoside as an unusual xanthine oxidase inhibitor
Vitale, R. M., Antenucci, L., Gavagnin, M., Raimo, G., & Amodeo, P. (2017) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2016.1252758 · Cited by 28 · see citing works
Analysis of Adaptation Mutants in the Hemagglutinin of the Influenza A(H1N1)pdm09 Virus
Jiménez-Alberto, A., Alvarado-Facundo, E., Ribas‐Aparicio, R. M., & Castelán-Vega, J. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0070005 · Cited by 27 · see citing works
Revealing the binding and drug resistance mechanism of amprenavir, indinavir, ritonavir, and nelfinavir complexed with HIV-1 protease due to double mutations G48T/L89M by molecular dynamics simulations and free energy analyses
Wang, R., Zhang, H., & Zheng, Q. (2020) · Physical Chemistry Chemical Physics · doi:10.1039/c9cp06657h · Cited by 27 · see citing works
Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives
Yang, B., Hamza, A., Chen, G., Wang, Y., & Zhan, C. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp1086416 · Cited by 25 · see citing works
Interdomain Interactions Modulate Collective Dynamics of the Metal-Binding Domains in the Wilson Disease Protein
Rodriguez-Granillo, A., Crespo, A., & Wittung-Stafshede, P. E. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp909450x · Cited by 25 · see citing works
Antigenic peptide molecular recognition by the DRB1–DQB1 haplotype modulates multiple sclerosis susceptibility
Kumar, A., Melis, P. M., Genna, V., Cocco, E. E., Marrosu, M. G., & Pieroni, E. (2014) · Molecular BioSystems · doi:10.1039/c4mb00203b · Cited by 24 · see citing works
Predicting antibody affinity changes upon mutations by combining multiple predictors
Kurumida, Y., Saitō, Y., & Kameda, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-76369-8 · Cited by 24 · see citing works
Identification Mechanism of BACE1 on Inhibitors Probed by Using Multiple Separate Molecular Dynamics Simulations and Comparative Calculations of Binding Free Energies
Wang, Y., Yang, F., Yan, D., Zeng, Y., Wei, B., Chen, J., & He, W. (2023) · Molecules · doi:10.3390/molecules28124773 · Cited by 24 · see citing works
Computational characterization of how the VX nerve agent binds human serum paraoxonase 1
Fairchild, S. Z., Peterson, M., Hamza, A., Zhan, C., Cerasoli, D. M., & Chang, W. E. (2010) · Journal of Molecular Modeling · doi:10.1007/s00894-010-0693-9 · Cited by 24 · see citing works
Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method
Wang, Y.-T., Su, Z., Hsieh, C.-H., & Chen, C. (2009) · Journal of Chemical Information and Modeling · doi:10.1021/ci9002238 · Cited by 24 · see citing works
Dynamical insights into the differential characteristics of Mycobacterium avium subsp. paratuberculosis peptide binding to HLA-DRB1 proteins associated with multiple sclerosis
Kumar, A., Sechi, L. A., Caboni, P., Marrosu, M. G., Atzori, L., & Pieroni, E. (2014) · New Journal of Chemistry · doi:10.1039/c4nj01903b · Cited by 23 · see citing works
Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism
Wang, R., & Zheng, Q. (2020) · Langmuir · doi:10.1021/acs.langmuir.0c02151 · Cited by 23 · see citing works
Chiral Indolylarylsulfone Non-Nucleoside Reverse Transcriptase Inhibitors as New Potent and Broad Spectrum Anti-HIV-1 Agents
Famiglini, V., Regina, G. L., Coluccia, A., Masci, D., Brancale, A., Badía, R., Riveira‐Muñoz, E., Esté, J. A., Crespan, E., Brambilla, A., et al. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b01906 · Cited by 23 · see citing works
Mangiferin is a new potential antimalarial and anticancer drug for targeting serine hydroxymethyltransferase
Maenpuen, S., Mee-udorn, P., Pinthong, C., Athipornchai, A., Phiwkaow, K., Watchasit, S., Pimviriyakul, P., Rungrotmongkol, T., Tinikul, R., Leartsakulpanich, U., et al. (2023) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2023.109712 · Cited by 22 · see citing works
Structural and Functional Analysis of Campylobacter jejuni PseG
Rangarajan, E. S., Proteau, A., Cui, Q., Logan, S. M., Potetinova, Z., Whitfield, D. M., Purisima, E. O., Cygler, M., Matte, A., Sulea, T. I., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.012351 · Cited by 22 · see citing works
Self-citation
Structural, energetic and lipophilic analysis of SARS-CoV-2 non-structural protein 9 (NSP9)
Araújo, J. D. O., Pinheiro, S., Zamora, W. J., Alves, C. N., Lameira, J., & Lima, A. H. (2021) · Scientific Reports · doi:10.1038/s41598-021-02366-0 · Cited by 21 · see citing works
Computational Prediction of 3,5-Diaryl-1H-Pyrazole and spiropyrazolines derivatives as potential acetylcholinesterase inhibitors for alzheimer disease treatment by 3D-QSAR, molecular docking, molecular dynamics simulation, and ADME-Tox
Alaouy, M. A. E., Alaqarbeh, M., Ouabane, M., Zaki, H., ElBouhi, M., Badaoui, H., Moukhliss, Y., Sbai, A., Maghat, H., Lakhlifi, T., et al. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2252116 · Cited by 21 · see citing works
Activity of chalcones derived from 2,4,5-trimethoxybenzaldehyde against Meloidogyne exigua and in silico interaction of one chalcone with a putative caffeic acid 3-O-methyltransferase from Meloidogyne incognita
Nunes, A. D. S., Campos, V. P., Mascarello, A., Stumpf, T. R., Chiaradia-Delatorre, L. D., Machado, A. R. T., Júnior, H. M. S., Yunes, R. A., Nunes, R. J., & de Oliveira, D. F. (2013) · Experimental Parasitology · doi:10.1016/j.exppara.2013.10.003 · Cited by 21 · see citing works
Structural and energetic basis of interaction between human estrogen-related receptor γ and environmental endocrine disruptors from multiple molecular dynamics simulations and free energy predictions
Chen, L., Huang, X., Li, Y., Zhao, B. Q., Liang, M., & Wang, R. (2022) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2022.130174 · Cited by 20 · see citing works
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
Sulea, T. I., Hogues, H., & Purisima, E. O. (2011) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-011-9529-7 · Cited by 20 · see citing works
Self-citation
Improving the Accuracy of Predicting protein–ligand binding-free Energy With Semiempirical Quantum Chemistry Charge
Peng, C., Wang, J., Yu, Y., Wang, G., Chen, Z., Xu, Z., Cai, T., Shao, Q., Shi, J., & Zhu, W. (2019) · Future Medicinal Chemistry · doi:10.4155/fmc-2018-0207 · Cited by 20 · see citing works
Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana
da Costa, C. H. S., Bichara, T. W., Gomes, G. C., dos Santos, A. M., da Costa, K. S., Lima, A. H., Alves, C. N., & Lameira, J. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1742206 · Cited by 20 · see citing works
Exploring the structural basis of the selective inhibition of monoamine oxidase A by dicarbonitrile aminoheterocycles: Role of Asn181 and Ile335 validated by spectroscopic and computational studies
Juárez‐Jiménez, J., Mendes, E., Galdeano, C., Martins, C., SILVA, D. N. N. D., Marco, J. L., Carreiras, M. C., Luque, F. J., & Ramsay, R. R. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.11.003 · Cited by 19 · see citing works
New indolylarylsulfone non-nucleoside reverse transcriptase inhibitors show low nanomolar inhibition of single and double HIV-1 mutant strains
Nalli, M., Rivera, J. I. A., Masci, D., Coluccia, A., Badía, R., Riveira‐Muñoz, E., Brambilla, A., Cinquina, E., Turriziani, O., Falasca, F., et al. (2020) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2020.112696 · Cited by 19 · see citing works
Computational study of bindings of HL9, a nonapeptide fragment of human lysozyme, to HIV-1 fusion protein gp41
Hartono, Y. D., Lee, A. N., Lee‐Huang, S., & Zhang, D. (2011) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2011.01.121 · Cited by 19 · see citing works
Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects
Zuo, Z., Gandhi, N. S., & Mancera, R. L. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci100321h · Cited by 18 · see citing works
Targeting the cell wall ofMycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem withL,D-transpeptidase 2
Silva, J. R. A., Bishai, W. R., Govender, T., Lamichhane, G., Maguire, G. E. M., Kruger, H. G., Lameira, J., & Alves, C. N. (2015) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2015.1029000 · Cited by 18 · see citing works
Naphthalene-based RNA Editing Inhibitor Blocks RNA Editing Activities and Editosome Assembly in Trypanosoma brucei
Moshiri, H., Acoca, S., Kala, S., Najafabadi, H. S., Hogues, H., Purisima, E. O., & Salavati, R. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.199646 · Cited by 18 · see citing works
Self-citation
Molecular modelling studies on Arylthioindoles as potent inhibitors of tubulin polymerization
Coluccia, A., Sabbadin, D., & Brancale, A. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.05.020 · Cited by 17 · see citing works
Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein
Darai, N., Mahalapbutr, P., Wolschann, P., Lee, V. S., Wolfinger, M. T., & Rungrotmongkol, T. (2022) · Scientific Reports · doi:10.1038/s41598-022-16252-w · Cited by 16 · see citing works
Theoretical study on the HIV-1 integrase–5CITEP complex based on polarized force fields
Wei, C., Mei, Y., & Zhang, D. (2010) · Chemical Physics Letters · doi:10.1016/j.cplett.2010.06.048 · Cited by 16 · see citing works
Mutagenesis and molecular dynamics simulations revealed the chitooligosaccharide entry and exit points for chitinase D from Serratia proteamaculans
Madhuprakash, J., Tanneeru, K., Karlapudi, B., Guruprasad, L., & Podile, A. R. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.06.014 · Cited by 16 · see citing works
Protein-ligand binding free energies from exhaustive docking.
Purisima, E., & Hogues, H. (2012) · Journal of Physical Chemistry B · doi:10.1021/jp212646s · Cited by 14 · see citing works
Self-citation
Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor
Naresh, G. K. R. S., & Guruprasad, L. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2032354 · Cited by 15 · see citing works
Optimizing electrostatic field calculations with the adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces. I. Sampling and focusing.
Ritchie, A. W., & Webb, L. J. (2013) · Journal of Physical Chemistry B · doi:10.1021/jp404582w · Cited by 15 · see citing works
Multiple Molecular Dynamics Simulations and Free-Energy Predictions Uncover the Susceptibility of Variants of HIV-1 Protease against Inhibitors Darunavir and KNI-1657
Wang, R., & Zheng, Q. (2021) · Langmuir · doi:10.1021/acs.langmuir.1c02348 · Cited by 14 · see citing works
Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?
Moustafa, I. M., Gohara, D. W., Uchida, A., Yennawar, N. H., & Cameron, C. E. (2015) · Viruses · doi:10.3390/v7112919 · Cited by 14 · see citing works
Solvated interaction energy: from small-molecule to antibody drug design
Purisima, E. O., Corbeil, C. R., Gaudreault, F., Wei, W., Deprez, C., & Sulea, T. I. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1210576 · Cited by 14 · see citing works
Self-citation
Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning
Yang, W., Wang, J., Zhao, L., & Chen, J. (2024) · Molecules · doi:10.3390/molecules29143377 · Cited by 13 · see citing works
Probing hot spots on protein-protein interfaces with all-atom free-energy simulation
Meliciani, I., Klenin, K. V., Strunk, T., Schmitz, K., & Wenzel, W. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3177008 · Cited by 13 · see citing works
Targeting Peptidyl-prolyl Cis-trans Isomerase NIMA-interacting 1: A Structure-based Virtual Screening Approach to Find Novel Inhibitors
da Costa, K. S., Galúcio, J. M. P., de Jesus, D. A., Gomes, G. C., Lima, A. H., Taube, P. S., dos Santos, A. M., & Lameira, J. (2019) · Current Computer - Aided Drug Design · doi:10.2174/1573409915666191025114009 · Cited by 13 · see citing works
Signal integration in the (m)TORC1 growth pathway
Ramlaul, K., & Aylett, C. H. S. (2018) · Frontiers in Biology · doi:10.1007/s11515-018-1501-7 · Cited by 12 · see citing works
Molecular docking and molecular dynamics simulation decoding molecular mechanism of EDCs binding to hERRγ
Sun, Y. X., Chen, L., Zhao, B., & Wang, R. (2024) · Journal of Molecular Modeling · doi:10.1007/s00894-024-05926-z · Cited by 12 · see citing works
Structural Considerations in the Fitness Landscape of a Virus
Watabe, T., & Kishino, H. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq056 · Cited by 12 · see citing works
Evaluation of the Wilma-SIE Virtual Screening Method in Community Structure–Activity Resource 2013 and 2014 Blind Challenges
Hogues, H., Sulea, T. I., & Purisima, E. O. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5b00278 · Cited by 12 · see citing works
Self-citation
Computed insight into a peptide inhibitor preventing the induced fit mechanism of MurA enzyme from Pseudomonas aeruginosa
Lima, A. H., dos Santos, A. M., Alves, C. N., & Lameira, J. (2016) · Chemical Biology & Drug Design · doi:10.1111/cbdd.12882 · Cited by 12 · see citing works
In vivo crystals reveal critical features of the interaction between cystic fibrosis transmembrane conductance regulator (CFTR) and the PDZ2 domain of Na+/H+ exchange cofactor NHERF1
Martin, E. R., Barbieri, A., Ford, R. C., & Robinson, R. C. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.012015 · Cited by 12 · see citing works
Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex
Dubey, K. D., & Ojha, R. P. (2011) · Journal of Molecular Modeling · doi:10.1007/s00894-011-1199-9 · Cited by 12 · see citing works
The Excellent Chemical Interaction Properties of Poloxamer and Pullulan with Alpha Mangostin on Amorphous Solid Dispersion System: Molecular Dynamics Simulation
Rusdin, A., Muchtaridi, M., Megantara, S., Wardhana, Y. W., Fakih, T. M., & Budiman, A. (2024) · Polymers · doi:10.3390/polym16213065 · Cited by 11 · see citing works
Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin
Correale, S., de Paola, I., Morgillo, C. M., Federico, A., Zaccaro, L., Pallante, P., Galeone, A., Fusco, A., Pedone, E. M., Luque, F. J., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0112082 · Cited by 11 · see citing works
Understanding the recognition mechanisms of Zα domain of human editing enzyme ADAR1 (hZαADAR1) and various Z-DNAs from molecular dynamics simulation
Wang, Q., Li, L., Wang, X., Liu, H., & Yao, X. (2014) · Journal of Molecular Modeling · doi:10.1007/s00894-014-2500-5 · Cited by 11 · see citing works
Molecular basis of the selective binding of MDMA enantiomers to the alpha4beta2 nicotinic receptor subtype: Synthesis, pharmacological evaluation and mechanistic studies
Llabrés, S., Garcia‐Ratés, S., Cristóbal‐Lecina, E., Riéra, A., Borrell, J. I., Camarasa, J., Pubill, D., Luque, F. J., & Escubedo, E. (2014) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2014.04.044 · Cited by 11 · see citing works
Free energy calculations of the interactions of c‐Jun‐based synthetic peptides with the c‐Fos protein
Zuo, Z., Gandhi, N. S., Arndt, K. M., & Mancera, R. L. (2012) · Biopolymers · doi:10.1002/bip.22099 · Cited by 11 · see citing works
Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods
Shi, S., Zhang, S., & Zhang, Q. (2015) · PLoS ONE · doi:10.1371/journal.pone.0141409 · Cited by 11 · see citing works
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding using Computational Alanine-Scanning Mutagenesis
Zheng, W., & Li, M. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2011.11.2003 · Cited by 9 · see citing works
In Silico and In Vitro Potential of FDA-Approved Drugs for Antimalarial Drug Repurposing against Plasmodium Serine Hydroxymethyltransferases
Mee-udorn, P., Phiwkaow, K., Tinikul, R., Sanachai, K., Maenpuen, S., & Rungrotmongkol, T. (2023) · ACS Omega · doi:10.1021/acsomega.3c01309 · Cited by 9 · see citing works
Novel Quinoline- and Naphthalene-Incorporated Hydrazineylidene–Propenamide Analogues as Antidiabetic Agents: Design, Synthesis, and Computational Studies
Alharbi, O. A., Alsaedi, W. H., Alsehli, M., Althagafi, S. H., Alharbi, H. Y., Asiri, Y. M., Ramu, R., & Al‐Ghorbani, M. (2024) · Pharmaceuticals · doi:10.3390/ph17121692 · Cited by 8 · see citing works
Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics
Bufano, M., Laudette, M., Blondeau, J., Lezoualc’h, F., Nalli, M., Silvestri, R., Brancale, A., & Coluccia, A. (2020) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-020-00332-y · Cited by 8 · see citing works

Factors That Affect the Computational Prediction of Hot Spots in Protein-Protein Complexes
Lin, J., Liu, P., Yang, H., & Vaidehi, N. (2012) · Computational Molecular Bioscience · doi:10.4236/cmb.2012.21003 · Cited by 4 · see citing works
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods
Lise, S., Archambeau, C., Pontil, M., & Jones, D. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-365 · Cited by 107 · see citing works
Probing the Effect of Point Mutations at Protein-Protein Interfaces with Free Energy Calculations
Almlöf, M., Åqvist, J., Smalås, A. O., & Brandsdal, B. O. (2005) · Biophysical Journal · doi:10.1529/biophysj.105.073239 · Cited by 63 · see citing works
Predicting single mutation effects on binding affinity at protein-protein interfaces based on MMPBSA calculationsPreprint
Noske, J., Lepoivre, T., Janzen, M., & Höcker, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.22.753561
Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes
Huang, D., Qi, Y., Song, J., & Zhang, J. Z. H. (2018) · Journal of Computational Chemistry · doi:10.1002/jcc.25592 · Cited by 26 · see citing works

Authors: Cui, Q., Sulea, T., Schrag, J. D., Munger, C., Hung, M.-N., Naïm, M., Cygler, M., & Purisima, E. O.
Affiliations: Biotechnology Research Institute (CA)
McGill University (CA)
Corresponding author: Purisima, Enrico O.
ORCID: Sulea, Traian
Purisima, Enrico O.
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2008-06
Volume: 379
Issue: 4
Pages: 787-802
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2008.04.035
OpenAlex: W2071919488
Cited by: 162
References: 56
Citations by year: 2026: 3 · 2025: 5 · 2024: 13 · 2023: 9 · 2022: 10 · 2021: 4 · 2020: 8 · 2019: 5 · 2018: 7 · 2017: 8 · 2016: 5 · 2015: 10 · 2014: 16 · 2013: 14 · 2012: 9
FWCI: 5.08
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
NPARC (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords: protein-protein interaction, MAPK signaling, alanine scanning, MM-GBSA, yeast two-hybrid, small molecule hits
MeSH terms: Binding Sites, Models, Molecular, Proteins, Recombinant Proteins, Thermodynamics, Mutagenesis, Site-Directed, Crystallography, X-Ray, Amino Acid Substitution, Two-Hybrid System Techniques, MAP Kinase Signaling System, Multiprotein Complexes, Adaptor Proteins, Signal Transducing, Protein Interaction Domains and Motifs

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks