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"Computers in Chemistry" ACS National Meeting - Free recorded webinars

7/15/2016

Over 200 recorded oral presentations from the 251st ACS National Meeting held in San Diego, CA are available at ACS Presentations on Demand.

The theme of this meeting was "Computers in Chemistry" so, the plenary session focused on Computational (Bio-)Chemistry achievements from world leaders in the field: Dr. George C. Schatz, Dr. Sharon Hammes-Schiffer, Dr. David Baker, and Dr. William L. Jorgensen.

Even if you missed the meeting, you can't miss these lectures available below!

William L. Jorgensen
30 years of free energy perturbation theory: From free energies of hydration to drug discovery

David Baker
Post-evolutionary biology: Design of novel protein structures, functions and assemblies

George C. Schatz
Using self-assembly to make functional materials: Computational perspectives

Sharon Hammes-Schiffer
Proton-coupled electron transfer in catalysis and energy conversion

Also:
Among the recordings from San Diego are the Kavli Foundation Lecture Series: Innovations in Chemistry (Dr. Emily Carter) and Emerging Leader in Chemistry (Dr. Rommie Amaro), speaking on

Computing cures: Enabling chemical discovery through the lens of a computational microscope

Zoe

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Ten Steps To Accelerate Your Bioinformatics Lab With Undergraduate Trainees

5/20/2013

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http://www.blueprint.org/Home/alumni/train-to-succeed

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Analysis of MD simulations using GROMACS tools

11/7/2012

5 Comments

I just came across this presentation which very nicely summarises the most important analysis tools for proteins available in Gromacs: Definitely worth reading and very good as a reference for experienced gromacs users.

Analysis tools that you can find in the presentation include:
- Looking at your trajectory
- Groups in analysis
- Root mean square deviations and fluctuations
- Radius of gyration and distances
- Hydrogen bonds
- Secondary structure analysis
- Free energy surfaces
- Principal component analysis: using Cartesian coordinates or dihedral angles
- Clustering

Evi

5 Comments

Structural Analysis and Verification Server

11/4/2012

2 Comments

The Structural Analysis and Verification Server performs the following functions:

1) Checks the stereochemical quality of a protein structure by analyzing residue-by-residue geometry and overall structure geometry. [Reference]

2) Does extensive checking of many sterochemical parameters of the residues in the model. [Reference]

3) Analyzes the statistics of non-bonded interactions between different atom types and plots the value of the error function versus position of a 9-residue sliding window, calculated by a comparison with statistics from highly refined structures. [Reference]

4) Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigned a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures. [Reference]

5) Calculates the volumes of atoms in macromolecules using an algorithm which treats the atoms like hard spheres and calculates a statistical Z-score deviation for the model from highly resolved (2.0 Å or better) and refined (R-factor of 0.2 or better) PDB-deposited structures. [Reference]

Zoe

2 Comments

PLoS Computational Biology: Ten Simple Rules

4/24/2012

0 Comments

This is a link to a very useful collection of articles written by PLoS Computational Biology Editor-in-Chief Philip E Bourne and collaborators, including:

Ten Simple Rules for Starting a Company

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia

Ten Simple Rules for Choosing between Industry and Academia

Ten Simple Rules for Graduate Students

Ten Simple Rules for Getting Grants

and many others!

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"Computers in Chemistry" ACS National Meeting - Free recorded webinars

Ten Steps To Accelerate Your Bioinformatics Lab With Undergraduate Trainees

Analysis of MD simulations using GROMACS tools

Structural Analysis and Verification Server

PLoS Computational Biology: Ten Simple Rules

Alexis, Maria, Dimitra, Ioannis, Michalis, Danai, Panos, George, Aspa, Zoe

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