相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13
Jorddy N. Cruz et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2019)
admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties
Hongbin Yang et al.
BIOINFORMATICS (2019)
PrankWeb: a web server for ligand binding site prediction and visualization
Lukas Jendele et al.
NUCLEIC ACIDS RESEARCH (2019)
CoMFA, CoMSIA, Topomer CoMFA, HQSAR, molecular docking and molecular dynamics simulations study of triazine morpholino derivatives as mTOR inhibitors for the treatment of breast cancer
Dhara M. Chhatbar et al.
COMPUTATIONAL BIOLOGY AND CHEMISTRY (2019)
I-TASSER gateway: A protein structure and function prediction server powered by XSEDE
Wei Zheng et al.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE (2019)
admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties (vol 52, pg 3099, 2012)
Feixiong Cheng et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2019)
High-performance medicine: the convergence of human and artificial intelligence
Eric J. Topol
NATURE MEDICINE (2019)
The BioGRID interaction database: 2019 update
Rose Oughtred et al.
NUCLEIC ACIDS RESEARCH (2019)
Metatox - Web application for generation of metabolic pathways and toxicity estimation
Anastasiya Rudik et al.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2019)
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
Polo C. -H. Lam et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2018)
PDBsum: Structural summaries of PDB entries
Roman A. Laskowski et al.
PROTEIN SCIENCE (2018)
Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents
Laurent R. Chiarelli et al.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2018)
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
Lukas Zimmermann et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
Consensus scoring model for the molecular docking study of mTOR kinase inhibitor
Dong-Dong Li et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2018)
In silico design of Mycobacterium tuberculosis epitope ensemble vaccines
Preksha Shah et al.
MOLECULAR IMMUNOLOGY (2018)
New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies
Elena Pini et al.
MOLECULES (2018)
CASTp 3.0: computed atlas of surface topography of proteins
Wei Tian et al.
NUCLEIC ACIDS RESEARCH (2018)
Mordred: a molecular descriptor calculator
Hirotomo Moriwaki et al.
JOURNAL OF CHEMINFORMATICS (2018)
Untargeted metabolomics reveals a new mode of action of pretomanid (PA-824)
Rafael Baptista et al.
SCIENTIFIC REPORTS (2018)
Exploring the possible binding mode of trisubstituted benzimidazoles analogues in silico for novel drug designtargeting Mtb FtsZ
Ding Li et al.
MEDICINAL CHEMISTRY RESEARCH (2017)
The ChEMBL database in 2017
Anna Gaulton et al.
NUCLEIC ACIDS RESEARCH (2017)
Alcohol consumption as a risk factor for tuberculosis: meta-analyses and burden of disease
Sameer Imtiaz et al.
EUROPEAN RESPIRATORY JOURNAL (2017)
PatchSearch: A Fast Computational Method for Off-Target Detection
Ines Rasolohery et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
MetaTox: Web Application for Predicting Structure and Toxicity of Xenobiotics' Metabolites
Anastasia V. Rudik et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening
Spencer S. Ericksen et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
The TB Portals: an Open-Access, Web-Based Platform for Global Drug-Resistant-Tuberculosis Data Sharing and Analysis
Alex Rosenthal et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2017)
Differential flap dynamics in L,D-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics
Zeynab Fakhar et al.
MOLECULAR BIOSYSTEMS (2017)
Exploring the substrate selectivity of human sEH and M. tuberculosis EHB using QM/MM
Sandra Rabi et al.
STRUCTURAL CHEMISTRY (2017)
Antitubercular Nitroimidazoles Revisited: Synthesis and Activity of the Authentic 3-Nitro Isomer of Pretomanid
Andrew M. Thompson et al.
ACS MEDICINAL CHEMISTRY LETTERS (2017)
In silico discovery and in vitro activity of inhibitors against Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase (Mtb BioA)
Junie B. Billones et al.
DRUG DESIGN DEVELOPMENT AND THERAPY (2017)
ChemSAR: an online pipelining platform for molecular SAR modeling
Jie Dong et al.
JOURNAL OF CHEMINFORMATICS (2017)
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY
Jade Shi et al.
SCIENTIFIC REPORTS (2017)
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
Antoine Daina et al.
SCIENTIFIC REPORTS (2017)
PyDescriptor: A new PyMOL plugin for calculating thousands of easily understandable molecular descriptors
Vijay H. Masand et al.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2017)
Development of a Novel Lead that Targets M. tuberculosis Polyketide Synthase 13
Anup Aggarwal et al.
CELL (2017)
Combinatorial chemistry in drug discovery
Ruiwu Liu et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2017)
Insight into the structural requirements of aminopyrimidine derivatives for good potency against both purified enzyme and whole cells of M-tuberculosis: combination of HQSAR, CoMSIA, and MD simulation studies
Auradee Punkvang et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2016)
HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
Sheng-You Huang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures
Michael A. Peabody et al.
NUCLEIC ACIDS RESEARCH (2016)
PubChem Substance and Compound databases
Sunghwan Kim et al.
NUCLEIC ACIDS RESEARCH (2016)
The drug binding sites and transport mechanism of the RND pumps from Mycobacterium tuberculosis: Insights from molecular dynamics simulations
Padmani Sandhu et al.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2016)
A Second, Druggable Binding Site in UDP-Galactopyranose Mutase from Mycobacterium tuberculosis?
Yun Shi et al.
CHEMBIOCHEM (2016)
Official American Thoracic Society/Centers for Disease Control and Prevention/Infectious Diseases Society of America Clinical Practice Guidelines: Treatment of Drug-Susceptible Tuberculosis
Payam Nahid et al.
CLINICAL INFECTIOUS DISEASES (2016)
Computer Aided Drug Design: Success and Limitations
Mohammad Hassan Baig et al.
CURRENT PHARMACEUTICAL DESIGN (2016)
SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening
Vincent Zoete et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
Picosecond to Millisecond Structural Dynamics in Human Ubiquitin
Kresten Lindorff-Larsen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Toward antituberculosis drugs: in silico screening of synthetic compounds against Mycobacterium tuberculosis L,D-transpeptidase 2
Junie B. Billones et al.
DRUG DESIGN DEVELOPMENT AND THERAPY (2016)
Tuberculosis
Madhukar Pai et al.
NATURE REVIEWS DISEASE PRIMERS (2016)
VirtualToxLab™ - In silico prediction of the toxic (endocrine-disrupting) potential of drugs, chemicals and natural products. Two years and 2,000 compounds of experience: a progress report
Angelo Vedani
ALTEX-Alternatives to Animal Experimentation (2016)
Docking-based virtual screening of known drugs against murE of Mycobacterium tuberculosis towards repurposing for TB
Sridharan Brindha et al.
BIOINFORMATION (2016)
Role of computer-aided drug design in modern drug discovery
Stephani Joy Y. Macalino et al.
ARCHIVES OF PHARMACAL RESEARCH (2015)
Beating the Millisecond Barrier in Molecular Dynamics Simulations
[Anonymous]
BIOPHYSICAL JOURNAL (2015)
Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations
Ramu Anandakrishnan et al.
BIOPHYSICAL JOURNAL (2015)
Managennent of latent Mycobacterium tuberculosis infection: WHO guidelines for Low tuberculosis burden countries
Haileyesus Getahun et al.
EUROPEAN RESPIRATORY JOURNAL (2015)
ZINC 15-Ligand Discovery for Everyone
Teague Sterling et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
DOCK 6: Impact of New Features and Current Docking Performance
William J. Allen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
Weijun Xu et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2015)
Molecular fingerprint similarity search in virtual screening
Adria Cereto-Massague et al.
METHODS (2015)
The I-TASSER Suite: protein structure and function prediction
Jianyi Yang et al.
NATURE METHODS (2015)
Treatment of Tuberculosis
C. Robert Horsburgh et al.
NEW ENGLAND JOURNAL OF MEDICINE (2015)
Latent Mycobacterium tuberculosis Infection
Haileyesus Getahun et al.
NEW ENGLAND JOURNAL OF MEDICINE (2015)
I-TASSER server: new development for protein structure and function predictions
Jianyi Yang et al.
NUCLEIC ACIDS RESEARCH (2015)
PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins
Hiba Abi Hussein et al.
NUCLEIC ACIDS RESEARCH (2015)
van der Waals forces in density functional theory: a review of the vdW-DF method
Kristian Berland et al.
REPORTS ON PROGRESS IN PHYSICS (2015)
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?
David Bajusz et al.
JOURNAL OF CHEMINFORMATICS (2015)
Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes
Gira Bhabha et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Smoking adversely affects treatment response, outcome and relapse in tuberculosis
Chi C. Leung et al.
EUROPEAN RESPIRATORY JOURNAL (2015)
Homology modeling: an important tool for the drug discovery
Tanos Celmar Costa Franca
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2015)
Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity
Elena Papaleo
FRONTIERS IN MOLECULAR BIOSCIENCES (2015)
3D-QSAR Approaches in Drug Design: Perspectives to Generate Reliable CoMFA Models
Cleber Camilo Melo-Filho et al.
CURRENT COMPUTER-AIDED DRUG DESIGN (2014)
Perspective: Fifty years of density-functional theory in chemical physics
Axel D. Becke
JOURNAL OF CHEMICAL PHYSICS (2014)
3D-QSAR CoMFA studies on sulfonamide inhibitors of the Rv3588c β-carbonic anhydrase from Mycobacterium tuberculosis and design of not yet synthesized new molecules
Shalini Singh et al.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY (2014)
Manganese(II) complexes with thiosemicarbazones as potential anti-Mycobacterium tuberculosis agents
Carolina G. Oliveira et al.
JOURNAL OF INORGANIC BIOCHEMISTRY (2014)
QSAR Modeling: Where Have You Been? Where Are You Going To?
Artem Cherkasov et al.
JOURNAL OF MEDICINAL CHEMISTRY (2014)
van der Waals density functional made accurate
Ikutaro Hamada
PHYSICAL REVIEW B (2014)
Global control of tuberculosis: from extensively drug-resistant to untreatable tuberculosis
Keertan Dheda et al.
LANCET RESPIRATORY MEDICINE (2014)
Discovery of Schaeffer's Acid Analogues as Lead Structures of Mycobacterium tuberculosis Type II Dehydroquinase Using a Rational Drug Design Approach
Marco F. Schmidt et al.
CHEMMEDCHEM (2013)
The holistic integration of virtual screening in drug discovery
Yusuf Tanrikulu et al.
DRUG DISCOVERY TODAY (2013)
An overview of the Amber biomolecular simulation package
Romelia Salomon-Ferrer et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2013)
Implications of Binding Mode and Active Site Flexibility for Inhibitor Potency against the Salicylate Synthase from Mycobacterium tuberculosis
Gamma Chi et al.
BIOCHEMISTRY (2012)
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment
Andrea Volkamer et al.
BIOINFORMATICS (2012)
Accounting for Induced-Fit Effects in Docking: What is Possible and What is Not?
Christoph A. Sotriffer
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2012)
Towards a new tuberculosis drug: pyridomycin - nature's isoniazid
Ruben C. Hartkoorn et al.
EMBO MOLECULAR MEDICINE (2012)
Recognizing Pitfalls in Virtual Screening: A Critical Review
Thomas Scior et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database
Ye Hu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17
Lars Ruddigkeit et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
Guoping Hu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties
Feixiong Cheng et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
K. Vanommeslaeghe et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
K. Vanommeslaeghe et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)
Surflex-Dock: Docking benchmarks and real-world application
Russell Spitzer et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)
PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure
David Ryan Koes et al.
NUCLEIC ACIDS RESEARCH (2012)
VirtualToxLab - A platform for estimating the toxic potential of drugs, chemicals and natural products
Angelo Vedani et al.
TOXICOLOGY AND APPLIED PHARMACOLOGY (2012)
OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia
Olga Tcheremenskaia et al.
Journal of Biomedical Semantics (2012)
Integration of Virtual and High Throughput Screening in Lead Discovery Settings
Timea Polgar et al.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2011)
Current Trends in Virtual High Throughput Screening Using Ligand-Based and Structure-Based Methods
Nagamani Sukumar et al.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2011)
Structure-based drug design to augment hit discovery
Subha Kalyaanamoorthy et al.
DRUG DISCOVERY TODAY (2011)
Integrating structure-based and ligand-based approaches for computational drug design
Gregory L. Wilson et al.
FUTURE MEDICINAL CHEMISTRY (2011)
Molecular Modeling of Mycobacterium Tuberculosis dUTpase: Docking and Catalytic Mechanism Studies
Teodorico C. Ramalho et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2011)
Pharmer: Efficient and Exact Pharmacophore Search
David Ryan Koes et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
FRED Pose Prediction and Virtual Screening Accuracy
Mark McGann
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
SwissParam: A Fast Force Field Generation Tool for Small Organic Molecules
Vincent Zoete et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Open3DQSAR: a new open-source software aimed at high-throughput chemometric analysis of molecular interaction fields
Paolo Tosco et al.
JOURNAL OF MOLECULAR MODELING (2011)
Link between Allosteric Signal Transduction and Functional Dynamics in a Multisubunit Enzyme: S-Adenosylhomocysteine Hydrolase
Yoonji Lee et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Predictive models for nucleoside bisubstrate analogs as inhibitors of siderophore biosynthesis in Mycobacterium tuberculosis: pharmacophore mapping and chemometric QSAR study
Nilesh R. Tawari et al.
MOLECULAR DIVERSITY (2011)
Ongoing and future developments at the Universal Protein Resource
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2011)
SwissDock, a protein-small molecule docking web service based on EADock DSS
Aurelien Grosdidier et al.
NUCLEIC ACIDS RESEARCH (2011)
Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery
Sean Ekins et al.
TRENDS IN MICROBIOLOGY (2011)
The MycoBrowser portal: A comprehensive and manually annotated resource for mycobacterial genomes
Adamandia Kapopoulou et al.
TUBERCULOSIS (2011)
Characterization and Transcriptome Analysis of Mycobacterium tuberculosis Persisters
Iris Keren et al.
MBIO (2011)
Algorithm improvements for molecular dynamics simulations
Per Larsson et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Comparison of Structure- and Ligand-Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors
Dennis M. Krueger et al.
CHEMMEDCHEM (2010)
Inhibition Studies of Mycobacterium tuberculosis Salicylate Synthase (Mbtl)
Alexandra Manos-Turvey et al.
CHEMMEDCHEM (2010)
Inhibitors of the Salicylate Synthase (MbtI) from Mycobacterium tuberculosis Discovered by High-Throughput Screening
Mahalakshmi Vasan et al.
CHEMMEDCHEM (2010)
Pharmacophore Based Drug Design Approach as a Practical Process in Drug Discovery
Qingzhi Gao et al.
CURRENT COMPUTER-AIDED DRUG DESIGN (2010)
Emerging Methods for Ensemble-Based Virtual Screening
Rommie E. Amaro et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic
Tanaji T. Talele et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
3D-QSAR in Drug Design - A Review
Jitender Verma et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation
Hanna Geppert et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)
Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
Oleg Trott et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
K. Vanommeslaeghe et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites
Peter Schmidtke et al.
JOURNAL OF MEDICINAL CHEMISTRY (2010)
Three-Dimensional Pharmacophore Methods in Drug Discovery
Andrew R. Leach et al.
JOURNAL OF MEDICINAL CHEMISTRY (2010)
I-TASSER: a unified platform for automated protein structure and function prediction
Ambrish Roy et al.
NATURE PROTOCOLS (2010)
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
Sheng-You Huang et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)
fpocket: online tools for protein ensemble pocket detection and tracking
Peter Schmidtke et al.
NUCLEIC ACIDS RESEARCH (2010)
e-LEA3D: a computational-aided drug design web server
Dominique Douguet
NUCLEIC ACIDS RESEARCH (2010)
Portrait of a Pathogen: The Mycobacterium tuberculosis Proteome In Vivo
Nicole A. Kruh et al.
PLOS ONE (2010)
Chemical space as a source for new drugs
Jean-Louis Reymond et al.
MEDCHEMCOMM (2010)
Fpocket: An open source platform for ligand pocket detection
Vincent Le Guilloux et al.
BMC BIOINFORMATICS (2009)
Structure-Based Virtual Ligand Screening: Recent Success Stories
Bruno O. Villoutreix et al.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING (2009)
Elucidating Isoniazid Resistance Using Molecular Modeling
Habibah A. Wahab et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Comparison of Nonbinary Similarity Coefficients for Similarity Searching, Clustering and Compound Selection
Aysha Al Khalifa et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
Oliver Korb et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
Jason B. Cross et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
Identifying and Characterizing Binding Sites and Assessing Druggability
Thomas A. Halgren
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility
Garrett M. Morris et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
CHARMM: The Biomolecular Simulation Program
B. R. Brooks et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
ROSETTALIGAND Docking with Full Ligand and Receptor Flexibility
Ian W. Davis et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
TB database: an integrated platform for tuberculosis research
T. B. K. Reddy et al.
NUCLEIC ACIDS RESEARCH (2009)
STRING 8-a global view on proteins and their functional interactions in 630 organisms
Lars J. Jensen et al.
NUCLEIC ACIDS RESEARCH (2009)
I-TASSER: Fully automated protein structure prediction in CASP8
Yang Zhang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Fast and accurate automatic structure prediction with HHpred
Andrea Hildebrand et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Exploring the Free Energy Landscape: From Dynamics to Networks and Back
Diego Prada-Gracia et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
John A. Capra et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
I-TASSER server for protein 3D structure prediction
Yang Zhang
BMC BIOINFORMATICS (2008)
Integrating Structure- and Ligand-Based Virtual Screening: Comparison of Individual, Parallel, and Fused Molecular Docking and Similarity Search Calculations on Multiple Targets
Lu Tan et al.
CHEMMEDCHEM (2008)
Applications of 2D Descriptors in Drug Design: A DRAGON Tale
Aliuska Morales Helguera et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2008)
What has virtual screening ever done for drug discovery?
David E. Clark
EXPERT OPINION ON DRUG DISCOVERY (2008)
Opportunities and challenges for HIV care in overlapping HIV and TB epidemics
Diane V. Havlir et al.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION (2008)
Comparison of similarity coefficients for clustering and compound selection
Maciej Haranczyk et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)
CHARMMing: A new, flexible web portal for CHARMM
Benjamin T. Miller et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)
Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM
Sunhwan Jo et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Recommendations for evaluation of computational methods
Ajay N. Jain et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2008)
PharmaGist: a webserver for ligand-based pharmacophore detection
Dina Schneidman-Duhovny et al.
NUCLEIC ACIDS RESEARCH (2008)
Insights into current limitations of density functional theory
Aron J. Cohen et al.
SCIENCE (2008)
DrugBank: a knowledgebase for drugs, drug actions and drug targets
David S. Wishart et al.
NUCLEIC ACIDS RESEARCH (2008)
LOCATE: a mammalian protein subcellular localization database
Josefine Sprenger et al.
NUCLEIC ACIDS RESEARCH (2008)
A similarity-based data-fusion approach to the visual characterization and comparison of compound databases
Jose L. Medina-Franco et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2007)
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
Markus Wiederstein et al.
NUCLEIC ACIDS RESEARCH (2007)
COBALT: constraint-based alignment tool for multiple protein sequences
Jason S. Papadopoulos et al.
BIOINFORMATICS (2007)
Docking of phosphonate and trehalose analog inhibitors into M. tuberculosis mycolyltransferase Ag85C: Comparison of the two scoring fitness functions GoldScore and ChemScore, in the GOLD software
Manoj Kumar Annamala et al.
BIOINFORMATION (2007)
eSLDB: eukaryotic subcellular localization database
Andea Pierleoni et al.
NUCLEIC ACIDS RESEARCH (2007)
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Tiqing Liu et al.
NUCLEIC ACIDS RESEARCH (2007)
PASS: identification of probable targets and mechanisms of toxicity
V. Poroikov et al.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH (2007)
Cheminformatics in Anti-Infective Agents Discovery
S. Sardari et al.
MINI-REVIEWS IN MEDICINAL CHEMISTRY (2007)
High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening
Theodora M. Steindl et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2006)
An official ATS statement: Hepatotoxicity of antituberculosis therapy
Jussi J. Saukkonen et al.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2006)
The structure of MbtI from Mycobacterium tuberculosis, the first enzyme in the biosynthesis of the siderophore mycobactin, reveals it to be a salicylate synthase
Anthony J. Harrison et al.
JOURNAL OF BACTERIOLOGY (2006)
BLAST: improvements for better sequence analysis
Jian Ye et al.
NUCLEIC ACIDS RESEARCH (2006)
FAF-Drugs: free ADME/tox filtering of compound collections
Maria A. Miteva et al.
NUCLEIC ACIDS RESEARCH (2006)
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
Joe Dundas et al.
NUCLEIC ACIDS RESEARCH (2006)
Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis
H Rachman et al.
INFECTION AND IMMUNITY (2006)
Blind docking of drug-sized compounds to proteins with up to a thousand residues
C Hetényi et al.
FEBS LETTERS (2006)
Docking and scoring - Theoretically easy, practically impossible?
B. Coupez et al.
CURRENT MEDICINAL CHEMISTRY (2006)
Kalign - an accurate and fast multiple sequence alignment algorithm
T Lassmann et al.
BMC BIOINFORMATICS (2005)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Scalable molecular dynamics with NAMD
JC Phillips et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
MetaSite: Understanding metabolism in human cytochromes from the perspective of the chemist
G Cruciani et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
Molecular dynamics simulation studies of the wild-type, I21V, and I16T mutants of isoniazid-resistant Mycobacterium tuberculosis enoyl reductase (InhA) in complex with NADH:: toward the understanding of NADH-InhA different affinities
EK Schroeder et al.
BIOPHYSICAL JOURNAL (2005)
The HHpred interactive server for protein homology detection and structure prediction
J Söding et al.
NUCLEIC ACIDS RESEARCH (2005)
ProFunc: a server for predicting protein function from 3D structure
RA Laskowski et al.
NUCLEIC ACIDS RESEARCH (2005)
Virtual computational chemistry laboratory - design and description
IV Tetko et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2005)
Comparison of automated docking programs as virtual screening tools
MD Cummings et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
Conformational changes associated with protein-protein interactions
CS Goh et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Accurate description of van der Waals complexes by density functional theory including empirical corrections
S Grimme
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
E Perola et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)
BLAST: at the core of a powerful and diverse set of sequence analysis tools
S McGinnis et al.
NUCLEIC ACIDS RESEARCH (2004)
Protein structure prediction and analysis using the Robetta server
DE Kim et al.
NUCLEIC ACIDS RESEARCH (2004)
The Database of Interacting Proteins: 2004 update
L Salwinski et al.
NUCLEIC ACIDS RESEARCH (2004)
Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
E Perola et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Approaches to measure chemical similarity - A review
N Nikolova et al.
QSAR & COMBINATORIAL SCIENCE (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm
GS Wu et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Improved protein-ligand docking using GOLD
ML Verdonk et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
CASTp: Computed atlas of surface topography of proteins
TA Binkowski et al.
NUCLEIC ACIDS RESEARCH (2003)
SWISS-MODEL: an automated protein homology-modeling server
T Schwede et al.
NUCLEIC ACIDS RESEARCH (2003)
Refinement of protein structures in explicit solvent
JP Linge et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Relibase:: Design and development of a database for comprehensive analysis of protein-ligand interactions
M Hendlich et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Principles of docking: An overview of search algorithms and a guide to scoring functions
I Halperin et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
The Binding Database: data management and interface design
X Chen et al.
BIOINFORMATICS (2002)
Consensus scoring for ligand/protein interactions
RD Clark et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2002)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)
Comparison of the NCI open database with seven large chemical structural databases
JH Voigt et al.
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2001)
Fast prediction and visualization of protein binding pockets with PASS
GP Brady et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2000)
A population-based survey of tuberculosis symptoms: How atypical are atypical presentations?
LG Miller et al.
CLINICAL INFECTIOUS DISEASES (2000)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)
分享论文
