From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine

Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data

(2012) Alexander Thielen et al.   INTERVIROLOGY

Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?

(2012) Thomas Lengauer   INTERVIROLOGY

Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project

(2012) Maurizio Zazzi et al.   INTERVIROLOGY

The HIVdb System for HIV-1 Genotypic Resistance Interpretation

(2012) Michele W. Tang et al.   INTERVIROLOGY

The “Virtual Patient” system: modeling cancer using deep sequencing technologies for personalized cancer treatment

(2012) Alexander Kühn et al.   Journal fur Verbraucherschutz und Lebensmittelsicherheit-Journal of Consumer Protection and Food Safety

Molecular Dynamics of HIV1-Integrase in Complex with93del—A Structural Perspective on the Mechanism of Inhibition

(2012) Miriam Sgobba et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Mechanism of Drug Efficacy Within the EGF Receptor Revealed by Microsecond Molecular Dynamics Simulation

(2012) S. Wan et al.   MOLECULAR CANCER THERAPEUTICS

NEW: Network-Enabled Wisdom in Biology, Medicine, and Health Care

(2012) E. E. Schadt et al.   Science Translational Medicine

Multiscale Cancer Modeling

(2011) Thomas S. Deisboeck et al.   Annual Review of Biomedical Engineering

Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate withIn VitroActivity

(2011) Barry C. Johnson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations

(2011) David W. Wright et al.   Journal of Chemical Information and Modeling

Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor

(2011) Shunzhou Wan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations

(2011) Haralambos Tzoupis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Reaction Kinetics of Catalyzed Competitive Heteropolymer Cleavage

(2011) S. Kashif Sadiq et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Does a Drug Molecule Find Its Target Binding Site?

(2011) Yibing Shan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

(2011) S. Wan et al.   Journal of the Royal Society Interface

Global landscape of HIV–human protein complexes

(2011) Stefanie Jäger et al.   NATURE

Computational Analysis of HIV-1 Resistance Based on Gene Expression Profiles and the Virus-Host Interaction Network

(2011) Tao Huang et al.   PLoS One

Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

(2011) Zhigang Liu et al.   PROTEIN JOURNAL

Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm

(2011) K. Marias et al.   Interface Focus

Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir

(2011) Li Xie et al.   PLoS Computational Biology

Network-Based Prediction and Analysis of HIV Dependency Factors

(2011) T. M. Murali et al.   PLoS Computational Biology

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

Specific HIV-1 integrase polymorphisms change their prevalence in untreated versus antiretroviral-treated HIV-1-infected patients, all naive to integrase inhibitors

(2010) Francesca Ceccherini-Silberstein et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

(2010) Simone Fulle et al.   Journal of Chemical Information and Modeling

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations

(2010) Rosemberg O. Soares et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Computational Mutation Scanning and Drug Resistance Mechanisms of HIV-1 Protease Inhibitors

(2010) Ge-Fei Hao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Retroviral intasome assembly and inhibition of DNA strand transfer

(2010) Stephen Hare et al.   NATURE

Rationalisation of the Differences between APOBEC3G Structures from Crystallography and NMR Studies by Molecular Dynamics Simulations

(2010) Flavia Autore et al.   PLoS One

Structure-based modeling of the functional HIV-1 intasome and its inhibition

(2010) L. Krishnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CCR5: From Natural Resistance to a New Anti-HIV Strategy

(2010) Lucia Lopalco   Viruses-Basel

Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks

(2010) Joel T. Dudley et al.   Journal of Cardiovascular Translational Research

Hybrid models of tumor growth

(2010) Katarzyna A. Rejniak et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

The value of drug repositioning in the current pharmaceutical market

(2009) E.L. Tobinick   DRUG NEWS & PERSPECTIVES

Impact on Replicative Fitness of the G48E Substitution in the Protease of HIV-1

(2009) Jean-Marie Zimmer et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance

(2009) Stefano Alcaro et al.   Journal of Chemical Information and Modeling

Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations

(2009) Anthony Ivetac et al.   JOURNAL OF MOLECULAR BIOLOGY

Gag Determinants of Fitness and Drug Susceptibility in Protease Inhibitor-Resistant Human Immunodeficiency Virus Type 1

(2009) C. M. Parry et al.   JOURNAL OF VIROLOGY

HIV decision support: from molecule to man

(2009) P.M.A. Sloot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

(2009) A. Bakan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

(2009) David L. Mobley et al.   STRUCTURE

Multiscale modeling for biologists

(2009) Martin Meier-Schellersheim et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Minority Quasispecies of Drug‐Resistant HIV‐1 That Lead to Early Therapy Failure in Treatment‐Naive and ‐Adherent Patients

(2008) Karin J. Metzner et al.   CLINICAL INFECTIOUS DISEASES

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Binding modes of CCR5-targetting HIV entry inhibitors: Partial and full antagonists

(2008) Ting Wang et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases

(2008) Ileana Stoica et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Turning promiscuous kinase inhibitors into safer drugs

(2008) Xi Zhang et al.   TRENDS IN BIOTECHNOLOGY

In silico cancer modeling: is it ready for prime time?

(2008) Thomas S Deisboeck et al.   Nature clinical practice. Oncology

Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations

(2002) Darón I. Freedberg et al.   PROTEIN SCIENCE