Macromolecular Modeling Blog ™

50 papers of potential interest from the (very) recent literature.

• Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Rita Santos et al

• Exploring Potency and Selectivity Receptor Antagonist Profiles Using a Multilabel Classification Approach: The Human Adenosine Receptors as a Key Study from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Lisa Michielan et al

• Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Eleanor J. Gardiner et al
  

• Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Gary Tresadern et al

• High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Simone Sciabola et al

• Rapid Comparison of Protein Binding Site Surfaces with Property Encoded Shape Distributions from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Sourav Das et al

• The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Tuomo Kalliokoski et al

• Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Ming Han et al

• Identification of Novel Non-Hydroxamate Anthrax Toxin Lethal Factor Inhibitors by Topomeric Searching, Docking and Scoring, and in Vitro Screening from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Ting-Lan Chiu et al

• Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model from Journal of Chemical Information and Modeling: Latest Articles (ACS Publications) by Debananda Das et al

• Prediction of protein binding sites in protein structures using hidden Markov support vector machine from BMC Bioinformatics – Latest articles by Xuan Wang

• SitesIdentify: a protein functional site prediction tool from BMC Bioinformatics – Latest articles by Jim Warwicker

• A generalized conformational energy function of DNA derived from molecular dynamics simulations from NAR by Yamasaki, S., Terada, T., Shimizu, K., Kono, H., Sarai, A.

• Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors from ChemMedChem by Dennis M. Krüger, Andreas Evers

• Synthesis, Enzymatic Evaluation, and Docking Studies of Fluorogenic Caspase 8 Tetrapeptide Substrates from ChemMedChem by Przemys[lstrok]aw Reszka, Riad Schulz, Karen Methling, Michael Lalk, Patrick J. Bednarski

• Discovery of Potent Vascular Endothelial Growth Factor Receptor-2 Inhibitors from ChemMedChem by Athanasios Papakyriakou, Maria E. Katsarou, Maria Belimezi, Michael Karpusas, Dionisios Vourloumis
  

• New Antimicrobial Hexapeptides: Synthesis, Antimicrobial Activities, Cytotoxicity, and Mechanistic Studies from ChemMedChem by Rohit K. Sharma, Sandeep Sundriyal, Nishima Wangoo, Werner Tegge, Rahul Jain

• Optimisation of Conoidin A, a Peroxiredoxin Inhibitor from ChemMedChem by Gu Liu, Catherine H. Botting, Kathryn M. Evans, Jeffrey A. G. Walton, Guogang Xu, Alexandra M. Z. Slawin, Nicholas J. Westwood

• SH2 domains: modulators of nonreceptor tyrosine kinase activity from Curr. op. in Struct. Biol. Panagis, Filippakopoulos , Susanne, Müller , Stefan, Knapp

• Structures of RNA polymerase–antibiotic complexes from Curr. op. in Struct. Biol. Mary X, Ho , Brian P, Hudson , Kalyan, Das , Eddy, Arnold , Richard H, Ebright

• The V119I polymorphism in protein L-isoaspartate O-methyltransferase alters the substrate-binding interface from PEDS by Rutherford, K., Daggett, V.

• Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis from PEDS by Tagami, U., Shimba, N., Nakamura, M., Yokoyama, K.-i., Suzuki, E.-i., Hirokawa, T.

• Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction from Protein Science by Yu Su, Ao Zhou, Xuefeng Xia, Wen Li, Zhirong Sun

• Disulfide conformation and design at helix N-termini from Proteins by S. Indu, Senthil T. Kumar, Sudhir Thakurela, Mansi Gupta, Ramachandra M. Bhaskara, C. Ramakrishnan, Raghavan Varadarajan
  

• Detection of multiscale pockets on protein surfaces using mathematical morphology from Proteins by Takeshi Kawabata

• Predicting protein complex geometries with a neural network from Proteins by Myong-Ho Chae, Florian Krull, Stephan Lorenzen, Ernst-Walter Knapp

• On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins from Proteins by Abdullah Kahraman, Richard J. Morris, Roman A. Laskowski, Angelo D. Favia, Janet M. Thornton

• Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: A statistical and theoretical study from Proteins by Xian-Hui Wu, Hui Zhang, Yun-Dong Wu

• MUFOLD: A new solution for protein 3D structure prediction from Proteins by Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan Kosztin, Yi Shang, Dong Xu

• Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels from Proteins by Andriy Anishkin, Adina L. Milac, H. Robert Guy
  

• HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch from Bioinformatics by Dlakic, M.

• LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction from Bioinformatics by Kauffman, C., Karypis, G.

• The interwinding nature of protein-protein interfaces and its implication for protein complex formation from Bioinformatics by Yura, K., Hayward, S.

• PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins from Bioinformatics by Oliva, R., Thornton, J. M., Pellegrini-Calace, M.

• EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures from Bioinformatics by Ghersi, D., Sanchez, R.

• Predicting Continuous Local Structure and the Effect of Its Substitution for Secondary Structure in Fragment-Free Protein Structure Prediction from Structure Eshel Faraggi, Yuedong Yang, Shesheng Zhang, Yaoqi Zhou.

• Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis from PLoS Computational Biology: New Articles by Wolfram Stacklies et al.

• A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome from PLoS Computational Biology: New Articles by Mu Gao et al.

• Design and Pharmacological Characterization of Inhibitors of Amantadine-Resistant Mutants of the M2 Ion Channel of Influenza A Virus from Biochemistry by Victoria Balannik et al

• Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations from Biochemistry by Daniel J. Sindhikara et al

• Metal Binding Affinities of Arabidopsis Zinc and Copper Transporters: Selectivities Match the Relative, but Not the Absolute, Affinities of their Amino-Terminal Domains from Biochemistry by Matthias Zimmermann et al

• ATP-Induced Conformational Changes in Hsp70: Molecular Dynamics and Experimental Validation of an in Silico Predicted Conformation from Biochemistry by Hyung-June Woo et al

• Thermodynamic Aspects of Coupled Binding and Folding of an Intrinsically Disordered Protein: A Computational Alanine Scanning Study from Biochemistry by L. Michel Espinoza-Fonseca

• Residue specific analysis of frustration in folding landscape of repeat ?/? protein apoflavodoxin from JMB Loren, Stagg , Antonios, Samiotakis , Dirar, Homouz , Margaret S., Cheung , Pernilla, Wittung-Stafshede

• Toward a quantitative theory of intrinsically disordered proteins and their function from PNAS by Liu, J., Faeder, J. R., Camacho, C. J.

• Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin from PNAS by Wlodarski, T., Zagrovic, B.

• Simultaneous prediction of protein folding and docking at high resolution from PNAS by Das, R., Andre, I., Shen, Y., Wu, Y., Lemak, A., Bansal, S., Arrowsmith, C. H., Szyperski, T., Baker, D.

• Finding of residues crucial for supersecondary structure formation from PNAS by Kister, A. E., Gelfand, I.

• Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations from PNAS by Noe, F., Schutte, C., Vanden-Eijnden, E., Reich, L., Weikl, T. R.

• A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins from PNAS by Pereira de Araujo, A. F., Onuchic, J. N.