Hydrophobic Binding Hot Spots of Bcl-xL Protein−Protein Interfaces by Cosolvent Molecular Dynamics Simulation

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

The BCL-2 protein family: opposing activities that mediate cell death

Youle, R. J., & Strasser, A. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2308 · Cited by 4,704 · see citing works

Reaching for high-hanging fruit in drug discovery at protein–protein interfaces

Wells, J. A., & McClendon, C. L. (2007) · Nature · doi:10.1038/nature06526 · Cited by 1,963 · see citing works

Structure of Bcl-x _L -Bak Peptide Complex: Recognition Between Regulators of Apoptosis

Sattler, M., Liang, H., Nettesheim, D., Meadows, R. P., Harlan, J. E., Eberstadt, M., Yoon, H. S., Shuker, S. B., Chang, B. S., Minn, A. J., et al. (1997) · Science · doi:10.1126/science.275.5302.983 · Cited by 1,476 · see citing works

The statistical-thermodynamic basis for computation of binding affinities: a critical review

Gilson, M. K., Given, J. A., Bush, B. L., & McCammon, J. A. (1997) · Biophysical Journal · doi:10.1016/s0006-3495(97)78756-3 · Cited by 1,222 · see citing works

Structural biology of the Bcl-2 family of proteins

Petros, A. M., Olejniczak, E. T., & Fesik, S. W. (2004) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2003.08.012 · Cited by 745 · see citing works

Crystal Structure of the Bcl-XL-Beclin 1 Peptide Complex

Oberstein, A., Jeffrey, P. D., & Shi, Y. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700492200 · Cited by 567 · see citing works

Binding in the growth hormone receptor complex.

Wells, J. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.1 · Cited by 439 · see citing works

Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies

Petros, A. M., Nettesheim, D. G., Wang, Y., Olejniczak, E. T., Meadows, R. P., Mack, J. C., Swift, K. M., Matayoshi, E. D., Zhang, H., Thompson, C. B., et al. (2000) · Protein Science · doi:10.1110/ps.9.12.2528 · Cited by 413 · see citing works

Apoptosis-based therapies for hematologic malignancies

Reed, J. C., & Pellecchia, M. (2005) · Blood · doi:10.1182/blood-2004-07-2761 · Cited by 402 · see citing works

The Structure of a Bcl-xL/Bim Fragment Complex

Liu, X., Dai, S., Zhu, Y., Marrack, P., & Kappler, J. W. (2003) · Immunity · doi:10.1016/s1074-7613(03)00234-6 · Cited by 358 · see citing works

Structural systems biology: modelling protein interactions

Aloy, P., & Russell, R. B. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1859 · Cited by 329 · see citing works

Crystal structure of ABT-737 complexed with Bcl-xL: implications for selectivity of antagonists of the Bcl-2 family

Lee, E. F., Czabotar, P. E., Smith, B. J., Deshayes, K., Zobel, K., Colman, P. M., & Fairlie, W. D. (2007) · Cell Death and Differentiation · doi:10.1038/sj.cdd.4402178 · Cited by 280 · see citing works

Locating and characterizing binding sites on proteins

Mattos, C., & Ringe, D. (1996) · Nature Biotechnology · doi:10.1038/nbt0596-595 · Cited by 256 · see citing works

Binding Site Detection and Druggability Index from First Principles

Seco, J., Luque, F. J., & Barril, X. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm801385d · Cited by 240 · see citing works

Protein–protein interactions as targets for small molecule drug discovery

Fry, D. C. (2006) · Biopolymers · doi:10.1002/bip.20608 · Cited by 203 · see citing works

The Diversity of Ubiquitin Recognition: Hot Spots and Varied Specificity

Winget, J. M., & Mayor, T. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.003 · Cited by 160 · see citing works

High‐Resolution Structural Characterization of a Helical α/β‐Peptide Foldamer Bound to the Anti‐Apoptotic Protein Bcl‐x L

Lee, E. F., Sadowsky, J., Smith, B. J., Czabotar, P. E., Peterson‐Kaufman, K. J., Colman, P. M., Gellman, S. H., & Fairlie, W. D. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200805761 · Cited by 159 · see citing works

Solvent dependence of dynamic transitions in protein solutions

Réat, V., Dunn, R. V., Ferrand, M., Finney, J., Daniel, R. M., & Smith, J. C. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.18.9961 · Cited by 124 · see citing works

Conformational Changes in Bcl-2 Pro-survival Proteins Determine Their Capacity to Bind Ligands

Lee, E. F., Czabotar, P. E., Yang, H. J., Sleebs, B. E., Lessène, G., Colman, P. M., Smith, B. J., & Fairlie, W. D. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.040725 · Cited by 87 · see citing works

Gateways to clinical trials

Tomillero, A., & Moral, M. A. (2008) · Methods and Findings in Experimental and Clinical Pharmacology · doi:10.1358/mf.2008.30.5.1236622 · Cited by 59 · see citing works

Organic Solvents Order the Dynamic Switch II in Ras Crystals

Buhrman, G., de Serrano, V. S., & Mattos, C. (2003) · Structure · doi:10.1016/s0969-2126(03)00128-x · Cited by 42 · see citing works

Effect of alcohols on protein hydration: crystallographic analysis of hen egg-white lysozyme in the presence of alcohols

Deshpande, A. A., Nimsadkar, S., & Mande, S. C. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905009364 · Cited by 37 · see citing works

Computational Analysis of Protein Hotspots

Yang, C., & Wang, S. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100026a · Cited by 32 · see citing works

Gateways to clinical trials. December 2008.

Tomillero, A., & Ma, M. (2008) · PubMed · Cited by 17 · see citing works

Modulators of Protein–Protein Interactions

Milroy, L.-G., Grossmann, T. N., Hennig, S., Brunsveld, L., & Ottmann, C. (2014) · Chemical Reviews · doi:10.1021/cr400698c · Cited by 497 · see citing works

Modulating protein–protein interactions: the potential of peptides

Nevola, L., & Giralt, E. (2014) · Chemical Communications · doi:10.1039/c4cc08565e · Cited by 291 · see citing works

State-of-the-art strategies for targeting protein–protein interactions by small-molecule inhibitors

Sheng, C., Dong, G., Miao, Z., Zhang, W., & Wang, W. (2015) · Chemical Society Reviews · doi:10.1039/c5cs00252d · Cited by 165 · see citing works

Discovery of A-1331852, a First-in-Class, Potent, and Orally-Bioavailable BCL-XL Inhibitor

Wang, L., Doherty, G. A., Judd, A. S., Tao, Z., Hansen, T. M., Frey, R. R., Song, X., Bruncko, M., Kunzer, A. R., Wang, X., et al. (2020) · ACS Medicinal Chemistry Letters · doi:10.1021/acsmedchemlett.9b00568 · Cited by 142 · see citing works

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

Raman, E. P., Yu, W., Lakkaraju, S. K., & MacKerell, A. D. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci4005628 · Cited by 137 · see citing works

Drug‐Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Villoutreix, B. O., Kuenemann, M. A., Poyet, J., Bruzzoni‐Giovanelli, H., Labbé, C. M., Lagorce, D., Spérandio, O., & Miteva, M. A. (2014) · Molecular Informatics · doi:10.1002/minf.201400040 · Cited by 114 · see citing works

Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics

Ghanakota, P., & Carlson, H. A. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b00399 · Cited by 114 · see citing works

A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation

Zhou, H., Lü, J., Liu, L., Bernard, D., Yang, C., Fernández‐Salas, E., Chinnaswamy, K., Layton, S. D., Stuckey, J. A., Yu, Q., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01243-7 · Cited by 103 · see citing works

In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets

Liao, J., Wang, Q., Wu, F., & Huang, Z. (2022) · Molecules · doi:10.3390/molecules27207103 · Cited by 97 · see citing works

Structure-Based Design of High-Affinity Macrocyclic Peptidomimetics to Block the Menin-Mixed Lineage Leukemia 1 (MLL1) Protein–Protein Interaction

Zhou, H., Liu, L., Huang, J., Bernard, D., Karataş, H., Navarro, A., Lei, M., & Wang, S. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm3015298 · Cited by 94 · see citing works

In silico structure-based approaches to discover protein-protein interaction-targeting drugs

Shin, W., Christoffer, C. W., & Kihara, D. (2017) · Methods · doi:10.1016/j.ymeth.2017.08.006 · Cited by 84 · see citing works

Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket

Pradhan, M. R., Siau, J. W., Kannan, S., Nguyen, M. N., Ouaray, Z., Kwoh, C. K., Lane, D. P., Ghadessy, F. J., & Verma, C. S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1314 · Cited by 62 · see citing works

Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application

Metz, A., Ciglia, E., & Gohlke, H. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212802651553 · Cited by 57 · see citing works

Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design

Faller, C. E., Raman, E. P., MacKerell, A. D., & Guvench, O. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2486-8_7 · Cited by 35 · see citing works

Computational close up on protein–protein interactions: how to unravel the invisible using molecular dynamics simulations?

Rakers, C., Bermúdez, M., Keller, B. G., Mortier, J., & Wolber, G. (2015) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1222 · Cited by 55 · see citing works

NMR Solution Structure of a Photoswitchable Apoptosis Activating Bak Peptide Bound to Bcl-x_L

Wysoczanski, P., Mart, R. J., Loveridge, E. J., Williams, C., Whittaker, S. B.-M., Crump, M. P., & Allemann, R. K. (2012) · Journal of the American Chemical Society · doi:10.1021/ja302390a · Cited by 47 · see citing works

Identification of Potential Small Molecule Allosteric Modulator Sites on IL-1R1 Ectodomain Using Accelerated Conformational Sampling Method

Yang, C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0118671 · Cited by 42 · see citing works

From proteomics to discovery of first-in-class ST2 inhibitors active in vivo

Ramadan, A. M., Daguindau, É., Rech, J. C., Chinnaswamy, K., Zhang, J., Hura, G. L., Griesenauer, B., Bolten, Z. T., Robida, A. M., Larsen, M. J., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.99208 · Cited by 42 · see citing works

Exploring the selectivity of inhibitor complexes with Bcl-2 and Bcl-XL: A molecular dynamics simulation approach

Wakui, N., Yoshino, R., Yasuo, N., Ohue, M., & Sekijima, M. (2017) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2017.11.011 · Cited by 43 · see citing works

Atranorin, an antimicrobial metabolite from lichen Parmotrema rampoddense exhibited in vitro anti-breast cancer activity through interaction with Akt activity

Harikrishnan, A., Veena, V., Lakshmi, B., Shanmugavalli, R., Theres, S., Prashantha, C. N., Shah, T., Oshin, K., Togam, R., & Nandi, S. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1734482 · Cited by 40 · see citing works

Analysis of Flexibility and Hotspots in Bcl-xL and Mcl-1 Proteins for the Design of Selective Small-Molecule Inhibitors

Yang, C., & Wang, S. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml200301w · Cited by 37 · see citing works

Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches

Kaan, H. Y. K., Sim, A. Y. L., Tan, S. K. J., Verma, C. S., & Song, H. (2017) · PLoS ONE · doi:10.1371/journal.pone.0178381 · Cited by 35 · see citing works

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions

Tan, Y. S., Spring, D. R., Abell, C., & Verma, C. S. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct5010577 · Cited by 32 · see citing works

Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations

Raman, E. P., Vanommeslaeghe, K., & MacKerell, A. D. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300088r · Cited by 29 · see citing works

Enrichment of Druggable Conformations from Apo Protein Structures Using Cosolvent-Accelerated Molecular Dynamics

Kalenkiewicz, A., Grant, B. J., & Yang, C. (2015) · Biology · doi:10.3390/biology4020344 · Cited by 29 · see citing works

Application of site-identification by ligand competitive saturation in computer-aided drug design

Goel, H., Hazel, A. J., Yu, W., Jo, S., & MacKerell, A. D. (2021) · New Journal of Chemistry · doi:10.1039/d1nj04028f · Cited by 25 · see citing works

Inhibitors of protein–protein interactions: New methodologies to tackle this challenge

Silvian, L. F., Enyedy, I. J., & Kumaravel, G. (2012) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2012.10.004 · Cited by 22 · see citing works

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design

You, W., Huang, Y. M. M., Kizhake, S., Natarajan, A., & Chang, C. A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005057 · Cited by 22 · see citing works

Druggability Assessment of Targets Used in Kinetic Target-Guided Synthesis

Ünver, M. Y., Gierse, R. M., Ritchie, H., & Hirsch, A. K. H. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00266 · Cited by 22 · see citing works

Computational functional group mapping for drug discovery

Guvench, O. (2016) · Drug Discovery Today · doi:10.1016/j.drudis.2016.06.030 · Cited by 20 · see citing works

Picornavirus VP3 protein induces autophagy through the TP53-BAD-BAX axis to promote viral replication

Mao, R., Zhu, Z., Yang, F., Sun, D., Zhou, X., Cao, W., Qin, X., Dang, W., Liu, H., Tian, H. W., et al. (2024) · Autophagy · doi:10.1080/15548627.2024.2350270 · Cited by 19 · see citing works

Hydrophobicity-induced prestaining for protein detection in polyacrylamide gel electrophoresis

Li, Z., Guan, W., Lu, C., Zhou, X., Luo, S., You, Y., & Ouyang, J. (2016) · Chemical Communications · doi:10.1039/c5cc09377e · Cited by 19 · see citing works

Dynamics of Bcl-xL in Water and Membrane: Molecular Simulations

Maity, A., Yadav, S., Verma, C. S., & Dastidar, S. G. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076837 · Cited by 17 · see citing works

Molecular Dynamics Simulation and Prediction of Druggable Binding Sites

Feng, T., & Barakat, K. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7756-7_6 · Cited by 16 · see citing works

Anti-leukemic, anti-lung, and anti-breast cancer potential of the microbial polyketide 2, 4-diacetylphloroglucinol (DAPG) and its interaction with the metastatic proteins than the antiapoptotic Bcl-2 proteins

Veena, V., Kennedy, K., Lakshmi, P., Krishna, R., & Sakthivel, N. (2016) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-016-2657-6 · Cited by 16 · see citing works

Computational Solvent Mapping in Structure-Based Drug Design

Hall, D. R., & Enyedy, I. J. (2015) · Future Medicinal Chemistry · doi:10.4155/fmc.14.155 · Cited by 15 · see citing works

Behavior of Solvent-Exposed Hydrophobic Groove in the Anti-Apoptotic Bcl-XL Protein: Clues for Its Ability to Bind Diverse BH3 Ligands from MD Simulations

Lama, D., Modi, V., & Sankararamakrishnan, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0054397 · Cited by 15 · see citing works

Gating by Tryptophan 73 Exposes a Cryptic Pocket at the Protein-Binding Interface of the Oncogenic eIF4E Protein

Lama, D., Brown, C. J., Lane, D. P., & Verma, C. S. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00812 · Cited by 14 · see citing works

The long unstructured region of Bcl‐xl modulates its structural dynamics

Priya, P., Maity, A., & Dastidar, S. G. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25316 · Cited by 14 · see citing works

Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity

Fischer, A., & Smieško, M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21020534 · Cited by 13 · see citing works

Modeling of Halogen–Protein Interactions in Co-Solvent Molecular Dynamics Simulations

Yang, Y., Mahmoud, A. H., & Lill, M. A. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00806 · Cited by 12 · see citing works

Solvent Sites Improve Docking Performance of Protein–Protein Complexes and Protein–Protein Interface-Targeted Drugs

Mayol, G. F., Defelipe, L. A., Arcon, J. P., Turjanski, A. G., & Marti, M. A. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00264 · Cited by 10 · see citing works

Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ-Dynamics

Mahmoud, A. H., Yang, Y., & Lill, M. A. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00940 · Cited by 10 · see citing works

Preparation, characterization, molecular docking and in vitro evaluation of two novel morin hydrate/CD inclusion complexes

Ren, S.-H., Zhang, J.-Q., Yan, H.-H., Zheng, X., Zhu, H., Jin, Y., & Lin, J. (2016) · Journal of Inclusion Phenomena and Macrocyclic Chemistry · doi:10.1007/s10847-016-0631-2 · Cited by 8 · see citing works

Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms

Zhao, M., Yu, W., & MacKerell, A. D. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03045 · Cited by 7 · see citing works

In vitro and in silico anti-leukemic activity of 2-amino-6-nitro-4-(4-oxo-2-thioxothiazolidin-5-yl)-4H-chromene-3-carbonitrile (ANC) through inhibition of anti-apoptotic Bcl-2 proteins

Veena, V., Choudhury, A. R., & Harikrishnan, A. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1893223 · Cited by 7 · see citing works

- Force-Field Representation of Biomolecular Systems

Small, M. C. (2015) · CRC Press eBooks · doi:10.1201/b18799-7 · Cited by 5 · see citing works

Force-Field Representation of Biomolecular Systems

Small, M. C., & MacKerell, A. D. (2015) · CRC Press eBooks · doi:10.1201/b18799-4 · Cited by 4 · see citing works

Computational Cosolvent Mapping Analysis Leads to Identify Salicylic Acid Analogs as Weak Inhibitors of ST2 and IL33 Binding

Yuan, X., Chinnaswamy, K., Stuckey, J. A., & Yang, C. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c00341 · Cited by 3 · see citing works

The glycine locating at random coil of picornaviruses VP3 enhances viral pathogenicity by targeting p53 to promote apoptosis and autophagyPreprint

Mao, R., Yang, F., Sun, D., Zhou, X., Zhu, Z., Guo, X., Liu, H., Tian, H., Zhang, K., Dang, W., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/718130 · Cited by 3 · see citing works

Site‐Identification by Ligand Competitive Saturation as a Paradigm of Co‐solvent MD Methods

Orr, A. A., & MacKerell, A. D. (2024) · Wiley eBooks · doi:10.1002/9783527840748.ch5 · Cited by 2 · see citing works

Overview of Protein-Protein Interactions and Small-Molecule Inhibitors Under Clinical Development

Dong, G., & Sheng, C. (2018) · Springer eBooks · doi:10.1007/978-981-13-0773-7_1 · Cited by 1 · see citing works

In Silico Approaches Assisting the Rational Design of Low Molecular Weight Protein–Protein Interaction Modulators

Villoutreix, B. O., Kuenemann, M. A., Lagorce, D., Spérandio, O., & Miteva, M. A. (2015) · CRC Press eBooks · doi:10.1201/b18799-21

Incorporating Hotspot Mapping and Allostery in Structure Based Drug Design.

Ghanakota, P. (2015) · Deep Blue (University of Michigan)

Inhibition of Biomarker ST2 by Small Molecules Improves Survival in Allogeneic Hematopoietic Cell TransplantationPreprint

Ramadan, A. M., Daguindau, É., Rech, J. C., Chinnaswamy, K., Zhang, J., Griesenauer, B., Bolten, Z. T., Robida, A. M., Larsen, M. J., Stuckey, J. A., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3155805

Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide HydrolasePreprint

Bzówka, M., Mitusińska, K., & Góra, A. (2020) · doi:10.21203/rs.3.rs-29814/v1

Structure-based design of antiviral drugs against respiratory viruses using in silico approaches

Ruano, L. C. (2024) · theses.fr (ABES) · doi:10.70675/434de13dz7ff8z46beza24ezfaf0740f7dea

BindingDB Entry 50012911: Discovery of A-1331852, a First-in-Class, Potent, and Orally-Bioavailable BCL-X

BindingDB (2022) · UC San Diego · doi:10.7270/q2542s8d

BindingDB Entry 50005241: Structure-based design of high-affinity macrocyclic peptidomimetics to block the menin-mixed lineage leukemia 1 (MLL1) protein-protein interaction.

BindingDB (2020) · UC San Diego · doi:10.7270/q22b91xm

BindingDB Entry 50002758: Druggability Assessment of Targets Used in Kinetic Target-Guided Synthesis.

BindingDB (2020) · UC San Diego · doi:10.7270/q2765j0c

Improving Small Molecule Docking for Bcl-xL via Accelerated Molecular Dynamics with Cosolvent

Kalenkiewicz, A., Yang, C., & Grant, B. J. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2014.11.1193

Enrichment of Druggable Conformations from Apo Protein Structures Using Cosolvent-Accelerated Molecular Dynamics

Kalenkiewicz, A., Grant, B. J., & Yang, C. (2015) · Biology · doi:10.3390/biology4020344 · Cited by 29 · see citing works

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

Bekker, G., Fukuda, I., Higo, J., Fukunishi, Y., & Kamiya, N. (2021) · Scientific Reports · doi:10.1038/s41598-021-84488-z · Cited by 22 · see citing works

Role of protein flexibility in the design of Bcl-XL targeting agents: insight from molecular dynamics

Novak, W., Wang, H., & Krilov, G. (2008) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-008-9237-0 · Cited by 13 · see citing works

Analysis of Flexibility and Hotspots in Bcl-xL and Mcl-1 Proteins for the Design of Selective Small-Molecule Inhibitors

Yang, C., & Wang, S. (2012) · ACS Medicinal Chemistry Letters · doi:10.1021/ml200301w · Cited by 37 · see citing works