a networked virtual environment ( nve ) is a computer - supported collaborative work ( cscw ) environment where multiple participants can interact with each other through computer networks for enhancing performances of their collaborations . since
, nve can overcome limit of time and space differences during face - to - face collaborations , nve has been widely researched for collaborative computer - aided design [ 1 , 2 ] . in a collaborative three - dimensional ( 3d ) computer - aided design ( cad )
system , distributed participants can work together in order for creating or modifying a 3d model in a virtual environment .
a 3d biomolecular modeling system is one of promising collaborative applications , and it has also been popularly researched and developed by various research groups . in order to design new materials and new drugs , we need to understand functions of proteins through analysis of a 3d protein structure at atomic resolution . first , it is generally determined by x - ray crystallography or nmr .
second , we can simulate the behaviors of the 3d molecules with equations of quantum and physics through computer simulations .
third , the 3d model of an enzyme , which is a candidate material or drug , can be used to design a higher binding affinity inhibitor against a target enzyme .
last , we can simulate the designed enzyme to have better characteristics such as higher activity and stability for industrial purpose [ 3 , 4 ] .   since molecular modeling is a large and complicated process
the participating biologists generally use their own favorite molecular modeling systems among many available systems .
therefore , real - time collaborations of the participating biologists using nve systems are not smoothly realized in general .   in this paper , we propose a collaborative experiment environment with different molecular modeling systems .
the environment consists of two collaborative systems , vrmms ( virtual reality molecular modeling system ) [ 57 ] and co - coot .
since the biologists can use their favorite systems with their designated roles , the proposed environment provides with a tunneling service for integrating the different collaborative applications .
there have been several researches on collaborative molecular modeling systems for studying and analyzing 3d biomolecular structures .
it performs molecular energy simulations , real - time monitoring , communication among participants , and document management .
biocore can also combined with existing software tools such as vmd   ( a visualization tool ) and namd   ( a computational system ) .
however , biocore strictly requires a high performance pc for effective and efficient exercises of collaborations , and the network system of biocore is not an open standard . as a result
, most researchers can not easily combine biocore with other applications . in our previous papers ,
vrmms was also coined a nve system to provide various collaborative device environments such as a cave and a laptop [ 6 , 7 ] .
it is specialized to edit 3d biomolecular structures for finding a best enzyme model in a crystallography process . using coot as a platform
, we developed a novel real - time collaboration tool , co - coot , to study 3d biomolecular structures .
co - coot can represent 3d structure models simultaneously at multiple displays in remote places , and enable multiple users to manipulate the models and conveniently communicate with other users with co - coot .
even though , co - coot is a good example of research approach to combine a collaboration module with existing open source software , it can restrict possible participations from other applications with different roles .
we designed a system architecture of the collaborative environment as a client / server network topology .
after the registration , other remote users can join the created project using co - coot or vrmms .
the participated clients can create various collaborative messages such as manipulation , rendering , editing , and ownership .
if the collaborative server receives the messages from user 1 , it directly distributes them to user 2 and also translates the co - coot format messages into the vrmms format messages for user 3 and user 4 .
the proposed agents of co - coot and vrmms provide open apis for the collaborative tunneling services .
the participating researchers can perform their collaboration simultaneously to share their intermediate experimental results , discuss a future direction , or solve their difficult problems via the proposed networked virtual environment .
the proposed environment offers a pessimistic concurrency control mechanism , which allows accesses and manipulates shared 3d molecular models with permission from the collaborative server . during the collaborative works ,
any user can request the collaborative server for his / her authority over a shared molecular model .
if other user already owns the shared molecular model , the server denies the request from the user .
the proposed networked virtual environment also provides a private workspace if the denied user still wants to manipulate the shared molecular model privately . with the private workspace
, the user can manipulate every features of the biomolecular model and the intermediate result can be stored in a file after using the private workspace . in order to provide transformations between two different applications ,
we analyzed both vrmms and co - coot in order to extract important functions in a collaborative 3d molecular modeling process .
we modeled six functions of vrmms and co - coot as described in tables 1 and 2 , respectively .  
table 1 shows the selected important functions of vrmms and table 2 shows the extracted important functions of co - coot .
function , the  file transferring  function , and the  chatting  function can be  equally  treated between vrmms and co - coot .
a user of vrmms can monitor 3d molecular models with various visualization methods such as wire frame , ball and stick , and surface modes in rendering function .
vrmms also provides a simulation function to calculate energy values of the 3d molecular models . in co - coot , a user can visualize molecular models as a wire frame mode .
so , a  surface  rendering model in vrmms can be converted and expressed as a 
the same conversion strategy can be applied to the  ball and stick  rendering model of vrmms . though vrmms has the  simulation  function , co - coot does not , on the other hand .
then , the simulation results from vrmms could be translated into a text format and read by the co - coot users as shown in figure 4 .
as described in table 1 , the proposed environment conducted through using a real molecular model .  
table 4 shows its related information such as its pdb code , name , and number of atoms .
first , we compared the rendering speed of co - coot and vrmms with various visualizations using the same molecular models .
the experiment was conducted on a desktop pc with core 2 quad cpu and an nvdia gtx 265 graphic card .
we tested rendering speeds of co - coot and vrmms for 100 seconds in terms of the fps ( frames per second ) values with four possible visualization modes .
as shown in figure 5 , the results showed a feasible rendering speed even though it is dependent on visualization modes or modeling systems .
second , we measured the number of transformations and average delivering times . in order to measure the values
, we conducted a collaborative molecular design process within different environments through network connections as shown in figure 6 .
the design computers were placed in different locations , and connected by a 10  mbps lan .
they conducted the collaborative design tasks as described in tables 1 and 2 for 40 minutes . 

a total number of transformed operations was 1004 , and most occurred transformations were manipulation and chatting as shown in figure 7(a ) .
as shown in figure 7(b ) , the proposed transformation strategies as described in table 3 showed different delivering performances .
manipulation , ownership , file transferring , and chatting showed fast delivery times . since modification needs more times to convert different data , the average delivering time of rendering showed medium performances .
simulation and editing generally showed the worst performances in the experiment because the proposed environment consumed lots of times to transform the operations .
however , they required more collaborative tunneling services such as a voice chatting and a sharing movie .
they also answered if the proposed environment could be applied to support other famous molecular modeling systems , then it would be feasible to utilize the proposed environment in the real collaborative molecular modeling processes .
in this paper , we propose a new collaborative molecular modeling environment to connect different modeling systems based on an approach with a collaborative tunneling service and transformation strategies . with our approach ,
the results of another performance evaluation of the pilot tests showed that the proposed environment could successfully transform collaboration data with stable delivering times through network .  
an additional user study showed that the participants would like to adopt the proposed system in their collaborative molecular modeling environment . for our future works
, we will expand the tunneling services to the other popular molecular modeling systems using ontology to support semantic transformation strategies .
 collaborative researches of three - dimensional molecular modeling can be limited by different time zones and locations . 
 a networked virtual environment can be utilized to overcome the problem caused by the temporal and spatial differences . however , 
 traditional approaches did not sufficiently consider integration of different computing environments , which were characterized by types of applications , roles of users , and so on . 
 we propose a collaborative molecular modeling environment to integrate different molecule modeling systems using a virtual tunneling service . 
 we integrated co - coot , which is a collaborative crystallographic object - oriented toolkit , with vrmms , which is a virtual reality molecular modeling system , through a collaborative tunneling system . 
 the proposed system showed reliable quantitative and qualitative results through pilot experiments . 