Herman W. T. van Vlijmen - Related publications

Medicinal Chemistry Leiden University, Leiden, Netherlands 
Computational Drug Discovery
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Ganotra GK, Nunes-Alves A, Wade RC. A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time. Methods in Molecular Biology (Clifton, N.J.). 2266: 171-186. PMID 33759127 DOI: 10.1007/978-1-0716-1209-5_10   
2021 Miller EB, Murphy RB, Sindhikara D, Borrelli KW, Grisewood MJ, Ranalli F, Dixon SL, Jerome S, Boyles NA, Day T, Ghanakota P, Mondal S, Rafi SB, Troast DM, Abel R, et al. Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding. Journal of Chemical Theory and Computation. PMID 33779166 DOI: 10.1021/acs.jctc.1c00136   
2021 Wang K, Zhou R, Li Y, Li M. DeepDTAF: a deep learning method to predict protein-ligand binding affinity. Briefings in Bioinformatics. PMID 33834190 DOI: 10.1093/bib/bbab072   
2021 Wang B, Su Z, Wu Y. Computational Assessment of Protein-Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes. Genomics, Proteomics & Bioinformatics. PMID 33838354 DOI: 10.1016/j.gpb.2021.03.004   
2021 Weng YL, Naik SR, Dingelstad N, Lugo MR, Kalyaanamoorthy S, Ganesan A. Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity. Scientific Reports. 11: 7429. PMID 33795718 DOI: 10.1038/s41598-021-86471-0   
2021 Shao G, Bao J, Pan X, He X, Qi Y, Zhang JZH. Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands. Frontiers in Molecular Biosciences. 8: 646524. PMID 33778009 DOI: 10.3389/fmolb.2021.646524   
2021 Ma N, Nivedha AK, Vaidehi N. Allosteric Communication Regulates Ligand-Specific GPCR Activity. The Febs Journal. PMID 33738925 DOI: 10.1111/febs.15826   
2021 Broni E, Kwofie SK, Asiedu SO, Miller WA, Wilson MD. A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of . Biomolecules. 11. PMID 33803906 DOI: 10.3390/biom11030458   
2021 Kim TY, Cha JS, Kim H, Choi Y, Cho HS, Kim HS. Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2. Computational and Structural Biotechnology Journal. 19: 1325-1334. PMID 33738081 DOI: 10.1016/j.csbj.2021.02.013   
2021 Kumar S, Kim MH. SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors. Journal of Cheminformatics. 13: 28. PMID 33766140 DOI: 10.1186/s13321-021-00507-1   
2021 Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL: in-depth assessment of structure quality and validation. Iucrj. 8: 238-256. PMID 33708401 DOI: 10.1107/S2052252521001159   
2021 Kumar R, Kumar R, Tanwar P. drug designing for COVID-19: an approach of high-throughput virtual screening, molecular, and essential dynamics simulations. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 33715592 DOI: 10.1080/07391102.2021.1897681   
2021 Fischer TF, Schoeder CT, Zellmann T, Stichel J, Meiler J, Beck-Sickinger AG. Cyclic Analogues of the Chemerin C-Terminus Mimic a Loop Conformation Essential for Activating the Chemokine-like Receptor 1. Journal of Medicinal Chemistry. PMID 33705662 DOI: 10.1021/acs.jmedchem.0c01804   
2021 Vittorio S, Gitto R, Adornato I, Russo E, De Luca L. In Silico Strategy for Targeting the mTOR Kinase at Rapamycin Binding Site by Small Molecules. Molecules (Basel, Switzerland). 26. PMID 33669763 DOI: 10.3390/molecules26041103   
2021 King E, Qi R, Li H, Luo R, Aitchison E. Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations. Journal of Chemical Theory and Computation. PMID 33764050 DOI: 10.1021/acs.jctc.0c01305   
2021 Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, et al. Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33723038 DOI: 10.1073/pnas.2012800118   
2021 Huai Z, Yang H, Sun Z. Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations. Journal of Computer-Aided Molecular Design. PMID 33759016 DOI: 10.1007/s10822-021-00382-w   
2021 Barge S, Jade D, Gosavi G, Talukdar NC, Borah J. In-silico screening for identification of potential inhibitors against SARS-CoV-2 transmembrane serine protease 2 (TMPRSS2). European Journal of Pharmaceutical Sciences : Official Journal of the European Federation For Pharmaceutical Sciences. 162: 105820. PMID 33775827 DOI: 10.1016/j.ejps.2021.105820   
2021 Sikkema HR, Poolman B. In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy. Scientific Reports. 11: 5756. PMID 33707507 DOI: 10.1038/s41598-021-85003-0   
2021 Ireland SM, Martin ACR. Zincbindpredict-Prediction of Zinc Binding Sites in Proteins. Molecules (Basel, Switzerland). 26. PMID 33673040 DOI: 10.3390/molecules26040966   
2021 Ireland SM, Martin ACR. Zincbindpredict-Prediction of Zinc Binding Sites in Proteins. Molecules (Basel, Switzerland). 26. PMID 33673040 DOI: 10.3390/molecules26040966   
2021 Shang J, Kojetin DJ. Structural mechanism underlying ligand binding and activation of PPARγ. Structure (London, England : 1993). PMID 33713599 DOI: 10.1016/j.str.2021.02.006   
2021 Ludwig J, Smith J, Pfaendtner J. Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin. The Journal of Physical Chemistry. B. PMID 33715376 DOI: 10.1021/acs.jpcb.1c00221   
2021 Mohanty AK, Choudhary S, Kaushik JK, Fisher AJ. Crystal structure of BRP39, a signaling glycoprotein expressed during mammary gland apoptosis at 2.6 Å resolution. Journal of Structural Biology. 107737. PMID 33838225 DOI: 10.1016/j.jsb.2021.107737   
2021 Halim SA, Sikandari AG, Khan A, Wadood A, Fatmi MQ, Csuk R, Al-Harrasi A. Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation. Biomolecules. 11. PMID 33671607 DOI: 10.3390/biom11020329   
2021 Naveed H, Reglin C, Schubert T, Gao X, Arold ST, Maitland ML. Identifying Novel Drug Targets by iDTPnd: A Case Study of Kinase Inhibitors. Genomics, Proteomics & Bioinformatics. PMID 33794377 DOI: 10.1016/j.gpb.2020.05.006   
2021 Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. Journal of Molecular Modeling. 27: 106. PMID 33694107 DOI: 10.1007/s00894-021-04721-4   
2021 Caldararu O, Blundell TL, Kepp KP. A base measure of precision for protein stability predictors: structural sensitivity. Bmc Bioinformatics. 22: 88. PMID 33632133 DOI: 10.1186/s12859-021-04030-w   
2021 Le HT, Do PC, Le L. Grafting Methionine on 1F1 Ab Increases the Broad-Activity on HA Structural-Conserved Residues of H1, H2, and H3 Influenza a Viruses. Evolutionary Bioinformatics Online. 17: 11769343211003082. PMID 33795930 DOI: 10.1177/11769343211003082   
2021 Di Rienzo L, Miotto M, Bò L, Ruocco G, Raimondo D, Milanetti E. Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network. Frontiers in Molecular Biosciences. 8: 626837. PMID 33718433 DOI: 10.3389/fmolb.2021.626837   
2021 Zheng W, Wen H. Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning. Proteins. PMID 33739482 DOI: 10.1002/prot.26075   
2021 Laurini E, Marson D, Aulic S, Fermeglia A, Pricl S. Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Acs Nano. PMID 33733740 DOI: 10.1021/acsnano.0c10833   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Fernandes DD, Neale C, Gomes GW, Li Y, Malik A, Pandey A, Orazietti AP, Wang X, Ye L, Scott Prosser R, Gradinaru CC. Ligand modulation of the conformational dynamics of the A adenosine receptor revealed by single-molecule fluorescence. Scientific Reports. 11: 5910. PMID 33723285 DOI: 10.1038/s41598-021-84069-0   
2021 Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. The Journal of Physical Chemistry. B. PMID 33818099 DOI: 10.1021/acs.jpcb.1c00972   
2021 Kaddouri Y, Abrigach F, Ouahhoud S, Benabbes R, El Kodadi M, Alsalme A, Al-Zaqri N, Warad I, Touzani R. Synthesis, characterization, reaction mechanism prediction and biological study of mono, bis and tetrakis pyrazole derivatives against Fusarium oxysporum f. sp. Albedinis with conceptual DFT and ligand-protein docking studies. Bioorganic Chemistry. 110: 104696. PMID 33652343 DOI: 10.1016/j.bioorg.2021.104696   
2021 Estrada Pabón JD, Haddox HK, Van Aken G, Pendleton IM, Eramian H, Singer JM, Schrier J. The Role of Configurational Entropy in Miniprotein Stability. The Journal of Physical Chemistry. B. PMID 33739115 DOI: 10.1021/acs.jpcb.0c09888   
2021 Browning C, McEwen AG, Mori K, Yokoi T, Moras D, Nakagawa Y, Billas IML. Nonsteroidal ecdysone receptor agonists use a water channel for binding to the ecdysone receptor complex EcR/USP. Journal of Pesticide Science. 46: 88-100. PMID 33746550 DOI: 10.1584/jpestics.D20-095   
2021 Kabir ML, Wang F, Clayton AHA. Red-Edge Excitation Shift Spectroscopy (REES): Application to Hidden Bound States of Ligands in Protein-Ligand Complexes. International Journal of Molecular Sciences. 22. PMID 33806656 DOI: 10.3390/ijms22052582   
2021 Khan A, Zia T, Suleman M, Khan T, Ali SS, Abbasi AA, Mohammad A, Wei DQ. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology. PMID 33755190 DOI: 10.1002/jcp.30367   
2021 Cao TQ, Kim JA, Woo MH, Min BS. SARS-CoV-2 main protease inhibition by compounds isolated from Luffa cylindrica using molecular docking. Bioorganic & Medicinal Chemistry Letters. 127972. PMID 33753260 DOI: 10.1016/j.bmcl.2021.127972   
2021 Aljoundi A, El Rashedy A, Soliman MES. Distinguishing the optimal binding mechanism through reversible and irreversible inhibition analysis of HSP72 protein in cancer therapy. Computers in Biology and Medicine. 132: 104301. PMID 33751994 DOI: 10.1016/j.compbiomed.2021.104301   
2021 Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. Journal of the American Chemical Society. PMID 33683866 DOI: 10.1021/jacs.0c09799   
2021 Vuorio J, Škerlová J, Fábry M, Veverka V, Vattulainen I, Řezáčová P, Martinez-Seara H. N-Glycosylation can selectively block or foster different receptor-ligand binding modes. Scientific Reports. 11: 5239. PMID 33664400 DOI: 10.1038/s41598-021-84569-z   
2021 Rahman T, Du Y, Zhao L, Shehu A. Generative Adversarial Learning of Protein Tertiary Structures. Molecules (Basel, Switzerland). 26. PMID 33668217 DOI: 10.3390/molecules26051209   
2021 Choi YK, Cao Y, Frank M, Woo H, Park SJ, Yeom MS, Croll TI, Seok C, Im W. Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of Chemical Theory and Computation. PMID 33689337 DOI: 10.1021/acs.jctc.0c01144   
2021 Dias D'Andréa É, Sebastian Retel J, Diehl A, Schmieder P, Oschkinat H, Ricardo Pires J. NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi. Journal of Structural Biology. 107715. PMID 33705979 DOI: 10.1016/j.jsb.2021.107715   
2021 Ploetz E, Schuurman-Wolters GK, Zijlstra N, Jager AW, Griffith DA, Guskov A, Gouridis G, Poolman B, Cordes T. Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ. Open Biology. 11: 200406. PMID 33823661 DOI: 10.1098/rsob.200406   
2021 Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of glutaminyl cyclase. Biological Chemistry. PMID 33823093 DOI: 10.1515/hsz-2020-0298   
2021 Wang D, Ge Y, Zhong B, Liu D. Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: implications for advanced antibody design. Computational and Structural Biotechnology Journal. PMID 33777333 DOI: 10.1016/j.csbj.2021.03.021