Identification of New Lead Molecules Against UBE2NL Enzyme for Cancer Therapy

[1]  Sarita Rajender Potlapally,et al.  Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery–a structure-based approach , 2017, Journal of chemical biology.

[2]  Bhargavi Kondagari,et al.  Suppressor of Cytokine Signalling‐3 as a Drug Target for Type 2 Diabetes Mellitus: A Structure‐Guided Approach , 2016 .

[3]  Ramasree Dulapalli,et al.  Homology modeling and virtual screening studies of FGF-7 protein—a structure-based approach to design new molecules against tumor angiogenesis , 2016, Journal of chemical biology.

[4]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[5]  J. Jeyakanthan,et al.  Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches , 2016, Journal of receptor and signal transduction research.

[6]  Venkata Ramana Reddy Chittireddy,et al.  Identification of Small Molecular Inhibitors for Efflux Protein: DrrA of Mycobacterium tuberculosis , 2015, Cellular and Molecular Bioengineering.

[7]  Lewis L. Lanier,et al.  NK cells and cancer: you can teach innate cells new tricks , 2015, Nature Reviews Cancer.

[8]  Adam D. Thomas,et al.  DNA damage and the balance between survival and death in cancer biology , 2015, Nature Reviews Cancer.

[9]  Dusanka Janezic,et al.  ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites , 2015, J. Chem. Inf. Model..

[10]  Sarita Rajender Potlapally,et al.  Homology modeling and virtual screening of ubiquitin conjugation enzyme E2A for designing a novel selective antagonist against cancer , 2015, Journal of receptor and signal transduction research.

[11]  A. Ciechanover.  The unravelling of the ubiquitin system , 2015, Nature Reviews Molecular Cell Biology.

[12]  Sarita Rajender Potlapally,et al.  Identification of novel leads applying in silico studies for Mycobacterium multidrug resistant (MMR) protein , 2014, Journal of biomolecular structure & dynamics.

[13]  Aihua Zhang,et al.  Metabolomics Approaches and Applications in Prostate Cancer Research , 2014, Applied Biochemistry and Biotechnology.

[14]  B. Banaganapalli,et al.  Molecular Modeling and Docking Studies of O-Succinylbenzoate Synthase of M. tuberculosis—a Potential Target for Antituberculosis Drug Design , 2014, Applied Biochemistry and Biotechnology.

[15]  R. Sandhir,et al.  Identification of Druggable Targets for Acinetobacter baumannii Via Subtractive Genomics and Plausible Inhibitors for MurA and MurB , 2013, Applied Biochemistry and Biotechnology.

[16]  N. Shabir,et al.  From Natural Products to Drugs for Epimutation Computer-Aided Drug Design , 2013, Applied Biochemistry and Biotechnology.

[17]  V. Morya,et al.  In Silico Study and Validation of Phosphotransacetylase (PTA) as a Putative Drug Target for Staphylococcus aureus by Homology-Based Modelling and Virtual Screening , 2012, Applied Biochemistry and Biotechnology.

[18]  Sara Schmitt,et al.  Targeting the ubiquitin-proteasome pathway: an emerging concept in cancer therapy. , 2011, Current topics in medicinal chemistry.

[19]  Tanya Singh,et al.  AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors , 2011, J. Chem. Inf. Model..

[20]  Sarah A. Teichmann,et al.  Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding , 2011, Structure.

[21]  Uma Vuruputuri,et al.  Identification of novel selective antagonists for cyclin C by homology modeling and virtual screening. , 2011, International journal of biological macromolecules.

[22]  Di Chen,et al.  The ubiquitin-proteasome system as a prospective molecular target for cancer treatment and prevention. , 2010, Current protein & peptide science.

[23]  Dusanka Janezic,et al.  ProBiS: a web server for detection of structurally similar protein binding sites , 2010, Nucleic Acids Res..

[24]  N. Foloppe,et al.  Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst , 2010, J. Chem. Inf. Model..

[25]  Nir Ben-Tal,et al.  Quality assessment of protein model-structures using evolutionary conservation , 2010, Bioinform..

[26]  Torsten Schwede,et al.  Automated comparative protein structure modeling with SWISS‐MODEL and Swiss‐PdbViewer: A historical perspective , 2009, Electrophoresis.

[27]  Thomas A. Halgren,et al.  Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..

[28]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[29]  W. Li,et al.  Polyubiquitin chains: functions, structures, and mechanisms , 2008, Cellular and Molecular Life Sciences.

[30]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..

[31]  Jóhannes Reynisson,et al.  Benchmarking the reliability of QikProp. Correlation between experimental and predicted values , 2008 .

[32]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[33]  Tom Halgren,et al.  New Method for Fast and Accurate Binding‐site Identification and Analysis , 2007, Chemical biology & drug design.

[34]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.

[35]  Ulf Norinder,et al.  Prediction of ADMET Properties , 2006, ChemMedChem.

[36]  Jian Ye,et al.  BLAST: improvements for better sequence analysis , 2006, Nucleic Acids Res..

[37]  J. Wade Harper,et al.  Drug discovery in the ubiquitin–proteasome system , 2006, Nature Reviews Drug Discovery.

[38]  Jie Liang,et al.  CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues , 2006, Nucleic Acids Res..

[39]  Jean-Christophe Nebel,et al.  Generation of 3D templates of active sites of proteins with rigid prosthetic groups , 2006, German Conference on Bioinformatics.

[40]  Ruth Nussinov,et al.  PatchDock and SymmDock: servers for rigid and symmetric docking , 2005, Nucleic Acids Res..

[41]  C. Lipinski.  Lead- and drug-like compounds: the rule-of-five revolution. , 2004, Drug discovery today. Technologies.

[42]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[43]  M. Congreve,et al.  A 'rule of three' for fragment-based lead discovery? , 2003, Drug discovery today.

[44]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[45]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[46]  T. Earnest,et al.  From words to literature in structural proteomics , 2003, Nature.

[47]  Krishna Sekar,et al.  Ramachandran plot on the web , 2002, Bioinform..

[48]  C. Ptak,et al.  Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. , 2001, Structure.

[49]  T. Ohta,et al.  The RING Heterodimer BRCA1-BARD1 Is a Ubiquitin Ligase Inactivated by a Breast Cancer-derived Mutation* , 2001, The Journal of Biological Chemistry.

[50]  W. Xiao,et al.  Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2–hUbc13 , 2001, Nature Structural Biology.

[51]  B. Wasylyk,et al.  The contribution of the RING finger domain of MDM2 to cell cycle progression , 2000, Oncogene.

[52]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

[53]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[54]  M J Sippl,et al.  Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.

[55]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[56]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[57]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[58]  G. Gonnet,et al.  Exhaustive matching of the entire protein sequence database. , 1992, Science.

[59]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[60]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[61]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[62]  Matthew L. Danielson,et al.  Computer-aided drug design platform using PyMOL , 2011, J. Comput. Aided Mol. Des..

[63]  A. Fiser.  Template-based protein structure modeling. , 2010, Methods in molecular biology.

[64]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[65]  Andrej Sali,et al.  Comparative Protein Structure Modeling and its Applications to Drug Discovery , 2004 .

[66]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[67]  Gisbert Schneider,et al.  Virtual screening and fast automated docking methods. , 2002, Drug discovery today.

[68]  Roman A. Laskowski,et al.  PDBsum: summaries and analyses of PDB structures , 2001, Nucleic Acids Res..

[69]  Andras Fiser,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.