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Last updated: 2008, April 20

    
~kuhn/ 12 pages
Protein Structural Analysis and Design Lab
Members of Leslie Kuhn's Group
publications1
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Main Directory
Protein Structural Analysis and Design Laboratory
Protein Structural Analysis and Design Lab
PSA Distributed Software
Lab Directory
Projects of Leslie's Group
Collaborations with other labs
PSDF at MSU - Course - Seminar
         
docs/ 1 pages
Consolv 1.0 Instructions
         
leslie/ 1 pages
http://35.8.152.15/~kuhn/leslie/cv.pdf
         
mike/ 2 pages
Mike's Project
Michael L. Raymer
         
paul/ 3 pages
Resume: Paul Sanschagrin
http://35.8.152.15/~kuhn/paul/Sanschagrin.thesis_screen.pdf
http://35.8.152.15/~kuhn/paul/Sanschagrin.thesis_print.pdf
         
pdf/ 5 pages
http://35.8.152.15/~kuhn/pdf/ProtSoc99_brandon1.pdf
http://35.8.152.15/~kuhn/pdf/ProtSoc99_brandon2.pdf
http://35.8.152.15/~kuhn/pdf/marburg01.paul.pdf
http://35.8.152.15/~kuhn/pdf/marburg01.maria.pdf
http://35.8.152.15/~kuhn/pdf/slide.pdf
         
people/ 28 pages
Homepage Leslie A. Kuhn
Homepage Mike Raymer
Homepage Paul Sanschagrin
Homepage Brandon M. Hespenheide
Homepage Maria Zavodszky
Homepage Trevor Barkham
PSA - Lab Alumni
PSA People Directory
Members of Leslie's Group
Homepage Litian He
Homepage Kanchan Champhekar
Homepage James Johnson
Homepage Soledad Quiroz
Homepage Rajesh Korde
Homepage Volker Schnecke
Homepage Mahesh Krishnaswamy
Homepage Amy Cayemberg
Homepage Yi Yang
Homepage Matt Larson
Homepage Vishal Thakkar
Homepage David Holstius
Homepage Michael Dahn
PSA - Carrie Barkham
Homepage Sandeep Namilikonda
Homepage Matthew Tonero
Homepage Jeffrey Van Voorst
Homepage Chetan Sukuru
Homepage Anjali Rohatgi
              
project_descriptions/ 4 pages
http://35.8.152.15/~kuhn/people/project_descriptions/Research_summary_maria.html
http://35.8.152.15/~kuhn/people/project_descriptions/Research_summary_litian.html
http://35.8.152.15/~kuhn/people/project_descriptions/Research_summary2_litian.html
http://35.8.152.15/~kuhn/people/project_descriptions/Research_summary_chetan.html
         
projects/ 20 pages
Research Project: Computational Screening of Molecular Databases
PSA - Phage-display Project
Secondary Interactions
Hydrogen bonds in protein flexibility and folding
PSA - Secondary Structure Assignment
PSA - DNA Polymerase Modeling - Fig 1
PSA - Water Site Cluster Analysis Project
PSA - KNN-GA/Water Prediction
Ligand Selectivity of the Estrogen Receptor
Research Project Matt Larson
Intersurf Project
Water Prediction
Funded Projects
PSA - Clustering - Fig 1
PSA - KNN-GA Figure
Water Prediction
Projects of PSA
PSA - ActiveSite GA Project
Research Project: Computational Screening of Molecular Databases
PSA - ActiveSite Pred GA - Fig 1
              
first/ 6 pages
ProFlex
User Tutorial
FIRST
Release Notes
Contact
FIRST
                   
docs/ 3 pages
http://35.8.152.15/~kuhn/projects/first/docs/FIRST_Manual.pdf
http://35.8.152.15/~kuhn/projects/first/docs/FIRST_comm_license.doc
http://35.8.152.15/~kuhn/projects/first/docs/ProFlex_GPL.txt
              
screening/ 7 pages
Project Directory
Research Project: Computational Screening of Molecular Databases
Peptide Screening
Database Screening with SLIDE
Multi-level indexing to accelerate docking
Collision resolving for docked ligands
Binding site solvation during screening in SLIDE v.2.3
                        
pdf/ 5 pages
http://35.8.152.15/~kuhn/projects/screening/publication_papers/pdf/Zavodszky_Kuhn_Proteins06.pdf
http://35.8.152.15/~kuhn/projects/screening/publication_papers/pdf/Zavodszky_Kuhn_PROTSCI_2005.pdf
http://35.8.152.15/~kuhn/projects/screening/publication_papers/pdf/Mueller_et_al_ProteinSci_2006_MS.pdf
http://35.8.152.15/~kuhn/projects/screening/publication_papers/pdf/Sukuru_et_al_JCAMD_rev_Mar_2006_MS.pdf
http://35.8.152.15/~kuhn/projects/screening/publication_papers/pdf/zavodszkyjcamd2002.pdf
              
slide/ 6 pages
Slide
Release Notes
User Manual
Tutorial
License Agreements
Contact
                   
Docs/ 5 pages
http://35.8.152.15/~kuhn/projects/slide/Docs/Slide_manual.pdf
http://35.8.152.15/~kuhn/projects/slide/Docs/Slide_Quick_Guide_updated_MIZ_20050119.pdf
http://35.8.152.15/~kuhn/projects/slide/Docs/SLIDE_flyer_200701.pdf
http://35.8.152.15/~kuhn/projects/slide/Docs/SLIDElicenseAcademic_v3_20070926.doc
http://35.8.152.15/~kuhn/projects/slide/Docs/SLIDElicCommercial_v3_20070926.doc
         
publication_papers/ 9 pages
Abstract: Threading and Structural Analysis of a Novel DNA Polymerase Subunit
Abstract: Prediction of the Active-Site Structure and NAD+ Binding in SQD1
Abstract: Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity
Abstract: Identification of mimotope peptides
Abstract: Ligand Screening with Side-chain Flexibility
Abstract: Cluster Analysis of Water Site in Thrombin and Trypsin
Abstract: The Role of Structure in Antibody Cross-Reactivity Between Peptides and Folded Proteins
Abstract: Simultaneous Feature Scaling and Selection Using a Genetic Algorithm
Abstract: Predicting Water-Mediated and Polar Interactions
              
pdf/ 38 pages
http://35.8.152.15/~kuhn/publication_papers/pdf/Kuhn_RSC2007_manuscript.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Mueller_et_al_ProteinSci_2006_MS.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Mueller_et_al_ProteinSci_2006_Figures.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Mueller_et_al_ProteinSci_2006_SupplMaterials.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Sukuru_et_al_JCAMD_rev_Mar_2006_MS.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Sukuru_et_al_JCAMD_rev_Mar_2006_SupplMaterials.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Zavodszky_Kuhn_PROTSCI_2005.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Lei_etal_JCC04.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Zavodszky_etal_Proteins04.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/Gohlke_etal_Proteins04.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/KronKuhn2003.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/raymerieee2003.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/zavodszkyjcamd2002.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/hespenheideprotsci2003.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/hespenheidejmgm2002.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/raderpnas2002.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/onesitebothfit2001.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/jacobsproteins2001.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/thorpejmgm2001.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/kuhn2000.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/raymer2000.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/hespenheidepsb2000.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/thorpepermath1999.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/jacobsrigidtheoryapp1999.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/tc1.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/garage96-04-01.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/atomicResidue1995.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/95ACA_drugdes.txt
http://35.8.152.15/~kuhn/publication_papers/pdf/19989.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/pnas99.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/science1999.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/ismb99.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/kuhn1999.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/schneckeproteins1997.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/kuhn1998.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/CraigJMB1998.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/garage97-02-05.pdf
http://35.8.152.15/~kuhn/publication_papers/pdf/raymerjmb1997.pdf
         
software/ 3 pages
PSA Distributed Software
PSA
http://35.8.152.15/~kuhn/software/temp_rock.html
              
WatCH/ 2 pages
WatCH Instructions
http://35.8.152.15/~kuhn/software/WatCH/license.txt
              
consolv/ 1 pages
Consolv 1.0 Instructions
              
sequery/ 3 pages
Sequery Information & Documentation -- Installation
Sequery Information & Documentation -- Use
Sequery Information & Documentation -- Installation
              
ssa/ 3 pages
SSA 3.0 Information & Documentation -- Installation
SSA 3.0 Information & Documentation -- Use
SSA 3.0 Information & Documentation -- Installation
         
volker/ 5 pages
Resume Volker Schnecke
Private Homepage Volker Schnecke
Publications Volker Schnecke
Research Project Volker Schnecke
Homecountry and -town Volker Schnecke
              
abstracts/ 20 pages
Abstract: Hybrid Genetic Algorithms for Solving Constrained Packing and Placement Problems
Abstract: Iterative Tiefensuche auf einem massiv parallelen System
Abstract: Ligand Screening with Side-chain Flexibility
Abstract: Hybrid Genetic Algorithms for Constrained Placement Problems
Abstract: Portable Parallelprogrammierung mit PVM
Abstract: Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity
Abstract: An Adaptive Parallel Genetic Algorithm for VLSI-Layout Optimization
Abstract: A Genetic Algorithm for VLSI Physical Design Automation
Abstract: Layoutgenerierung mit genetischen Algorithmen
Abstract: Genetic Design of VLSI-Layouts
Abstract: Portability versus Efficiency? Parallel Applications on PVM and Parix
Abstract: Performance on PVM on a Highly Parallel Transputer System
Abstract: Iterative Tiefensuche auf einem massiv parallelen System
Abstract: Work Load Balancing in Highly Parallel Depth-First Search
Abstract: AIDA* - Asynchronous Parallel IDA*
Abstract: Screening for Flexible Organic Ligands
Abstract: Screening for Flexible Ligands with Solvation
Abstract: Screening for Potential Ligands to Proteins with Inducible Side-chain Complementarity
Abstract: Screening Ligand Databases for Potential Ligands to Protein Active Sites
Abstract: Screening and Docking of Flexible Organic Ligands to Solvated Binding Sites with Induced Complementarity
                   
boston/ 1 pages
Presentation at the Protein Society Symposium, Boston, MA, July 1997
                   
sf/ 1 pages
Presentation at the USCF-MDI Meeting on Docking and Scoring, February 1998
              
pdf/ 6 pages
http://35.8.152.15/~kuhn/volker/pdf/tc_paper.pdf
http://35.8.152.15/~kuhn/volker/pdf/ieee_ec.pdf
http://35.8.152.15/~kuhn/volker/pdf/ismb99.pdf
http://35.8.152.15/~kuhn/volker/pdf/sd_specitope.pdf
http://35.8.152.15/~kuhn/volker/pdf/sf_specitope.pdf
http://35.8.152.15/~kuhn/volker/pdf/marburg99.pdf